From ffe926d5cabc67569e3baf73d4eaaf862ddefd0a Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@bils.se>
Date: Mon, 24 Sep 2018 10:51:58 +0200
Subject: [PATCH] add MAKER exercice for ELIXIR GAA

---
 _pages/annotation.md                          |   2 +-
 .../Eugene/exercice_eugene_appliance.md       | 235 +++++++++++++
 .../IFBcloud/create_IFB_cloud_user_account.md |  72 ++++
 .../IFBcloud/use_IFB_cloud_appliance.md       |  82 +++++
 .../MAKER/StructuralAnnotation_mtp.md         | 330 ++++++++++++++++++
 _pages/annotation/MAKER/inspect_the_output.md |  37 ++
 _pages/annotation/MAKER/inspect_the_result.md |  49 +++
 .../MAKER/practical2_supl3_maker.md           |  52 +++
 .../annotation/MAKER/practical2_supl_maker.md |  50 +++
 9 files changed, 908 insertions(+), 1 deletion(-)
 create mode 100644 _pages/annotation/Eugene/exercice_eugene_appliance.md
 create mode 100644 _pages/annotation/IFBcloud/create_IFB_cloud_user_account.md
 create mode 100644 _pages/annotation/IFBcloud/use_IFB_cloud_appliance.md
 create mode 100644 _pages/annotation/MAKER/StructuralAnnotation_mtp.md
 create mode 100644 _pages/annotation/MAKER/inspect_the_output.md
 create mode 100644 _pages/annotation/MAKER/inspect_the_result.md
 create mode 100644 _pages/annotation/MAKER/practical2_supl3_maker.md
 create mode 100644 _pages/annotation/MAKER/practical2_supl_maker.md

diff --git a/_pages/annotation.md b/_pages/annotation.md
index 0db916b6..2478fc03 100644
--- a/_pages/annotation.md
+++ b/_pages/annotation.md
@@ -52,7 +52,7 @@ Basic knowledge of Linux (Linux for dummies required) - TOGGLe practical
 <h3>Training material</h3>
 <ul>
 <li>Practice Annotation : <a target="_blank" href="{{ site.url }}/annotation/IFB-EGNEPpractice">see</a></li>
-  
+<li>Practice Annotation MAKER : <a target="_blank" href="{{ site.url }}/annotation/MAKER/StructuralAnnotation_mtp.md>see</a></li>  
 </ul>
 </div>
 
diff --git a/_pages/annotation/Eugene/exercice_eugene_appliance.md b/_pages/annotation/Eugene/exercice_eugene_appliance.md
new file mode 100644
index 00000000..b8968333
--- /dev/null
+++ b/_pages/annotation/Eugene/exercice_eugene_appliance.md
@@ -0,0 +1,235 @@
+# EGNEP run
+
+**************************
+**Author(s)**: Stéphanie Bocs, Laurent Bouri, Jacques Dainat
+
+**Date**: 15/09/2018
+
+**Keywords**: eugene, eukaryotic gene annotation pipeline
+
+**Description**: Reproducible run of Eugene eukaryotic pipeline on IFB cloud appliancee
+**********
+
+<!-- TOC depthFrom:2 depthTo:2 withLinks:1 updateOnSave:1 orderedList:0 -->
+
+- [EGNEP run](#egnep-run)
+- [EGNEP error](#egnep-error)
+- [EGNEP kill](#egnep-kill)
+
+<!-- /TOC -->
+
+## Prerequisite
+
+1. You need an account on the IFB could. If you don't have any please refer to the following documentation:
+[How to create an account on the IFB cloud](create_IFB_cloud_user_account)
+
+2. You need to be connected to an Eugene appliance with **8 CPU et 32 Go de RAM**. If it is not the case, please refer to the following documentation:
+[How to launch and use an appliance on the IFB could](use_IFB_cloud_appliance)
+
+## Excercise (From an Eugene IFB coud appliance)
+
+### 1) Preparing your data
+
+For software licence reasons, transfer the transposable element polypeptide file, for instance
+
+     Downloads SIDIBEBOCS$ scp repbase20.05_aaSeq_cleaned_TE.fa root@134.158.247.40:/root/bank_tair/
+
+From your the root terminal of your appliance, index the databanks
+
+     	cd /root/bank_tair/
+	makeblastdb -in TAIR_est2.fasta -dbtype nucl
+	makeblastdb -in repbase20.05_aaSeq_cleaned_TE.fa -dbtype prot
+	makeblastdb -in uniprot-thaliana_swiss2.fasta -dbtype prot -parse_seqids
+	makeblastdb -in uniprot-thaliana_trembl2.fasta -dbtype prot -parse_seqids
+
+### 2) Running & checking
+Run EGNEP (without --no_red option)
+
+     # cd
+     # nohup time $EGNEP/bin/int/egn-euk.pl --indir /root/input_dir/ --outdir /root/output_dir/ --cfg /root/bank_tair/egnep-test.cfg --workingdir /root/work_dir/ >& pipeline.txt &
+
+Check the progress of the run
+```bash
+# less pipeline.txt 
+# tail -f pipeline.txt
+nohup: ignoring input
+################################################################################
+################################################################################
+# /usr/bin/egnep-1.4/bin/int/egn-euk.pl --no_red --indir /root/input_dir/ --outdir /root/output_dir/ --cfg /root/bank_tair/egnep-test.cfg --workingdir /root/w
+ork_dir
+# EuGene Pipeline EUK - version 1.4
+# EUGENEDIR /usr/bin/eugene-4.2a
+# EGNEP /usr/bin/egnep-1.4
+# Log file /root/work_dir/logger.1536421660.26448.txt
+################################################################################
+################################################################################
+
+Create tree.....................................................................started
+Create tree.....................................................................done
+#########################  Protein database cleaning  ##########################
+root@machine1a957191-dcc3-4d5e-83d7-e97d29f17266:~# tail -f pipeline.txt 
+# EuGene Pipeline EUK - version 1.4
+# EUGENEDIR /usr/bin/eugene-4.2a
+# EGNEP /usr/bin/egnep-1.4
+# Log file /root/work_dir/logger.1536421660.26448.txt
+################################################################################
+################################################################################
+
+Create tree.....................................................................started
+Create tree.....................................................................done
+#########################  Protein database cleaning  ##########################
+#####################  Protein sequence similarity search  #####################
+BlastX uniprot-thaliana_swiss2.fasta uniprot-thaliana_trembl2.fasta.............started
+  BLASTX PARAMETERS=-outfmt 6 -evalue 0.01 -gapopen 9 -gapextend 2 -max_target_seqs 500000 -max_intron_length 15000  -seg yes
+  UBLAST PARAMETERS=-threads 8 -evalue 1 -lopen 9 -lext 2 -accel 1
+```
+
+## EGNEP error
+
+### 1) Variables
+
+The environment variables should be already set
+ 
+     # export EUGENEDIR=/usr/bin/eugene-4.2a
+     # export EGNEP=/usr/bin/egnep-1.4
+
+### 2) Index databanks
+
+The database "/root/bank_tair/uniprot-thaliana_swiss2.fasta" does not exist or isn't indexed. (Use 'makeblastdb' program to index).
+
+The database "/root/bank_tair/uniprot-thaliana_trembl2.fasta" does not exist or isn't indexed. (Use 'makeblastdb' program to index).
+
+### 3) Program missing
+
+=>The value of the parameter prg_rnammer is >/usr/bin/egnep-1.4/bin/ext/rnammer< which is not a name of an existing and non empty file at /usr/bin/egnep-1.4/bin/int/egn-euk.pl line 2207.
+Command exited with non-zero status 25
+
+```bash
+cd /usr/bin/egnep-1.4/bin/ext/
+lrwxrwxrwx  1 root   root        17 Aug 27 15:14 bedtools2 -> bedtools2-2.24.0/
+drwxrwxr-x 11 root   root      4096 Aug 27 15:12 bedtools2-2.24.0
+drwxr-xr-x  4 root   root      4096 Aug 27 15:12 bin
+-rwxrwxr-x  1    339 ubuntu   55318 Feb 24  2017 BioFileConverter.pl
+drwxrwxr-x  5    339 ubuntu    4096 Feb 24  2017 blast-2.2.26
+-rwxrwxr-x  1    339 ubuntu    2509 Feb 24  2017 convert_rfam2gff3.pl
+-rwxrwxr-x  1    339 ubuntu    2280 Feb 24  2017 convert_rnammer2gff3.pl
+-rwxrwxr-x  1    339 ubuntu    2813 Feb 24  2017 convert_trnascan2gff3.pl
+lrwxrwxrwx  1 root   root        17 Aug 27 15:12 genometools -> genometools-1.5.6
+drwxrwxr-x 15 root   root      4096 Aug 27 15:12 genometools-1.5.6
+lrwxrwxrwx  1 root   root        15 Aug 27 15:22 gmap -> gmap-2017-02-15
+drwxr-xr-x  7  11414   1279    4096 Aug 27 15:22 gmap-2017-02-15
+drwxrwxr-x 13 990287  93203    4096 Mar  4  2015 hmmer-3.1b2-linux-intel-x86_64
+drwxr-xr-x  3 root   root      4096 Aug 27 15:12 include
+drwxr-xr-x 10  41650  93203    4096 Aug 27 15:08 infernal-1.1.1
+drwxr-xr-x  3   2314 cdrom     4096 Jul  4  2006 lib
+-rwxr-xr-x  1   2314 cdrom        0 Jul 24  2007 LICENSE
+-rwxrwxr-x  1    339 ubuntu    9931 Feb 24  2017 lipm_bed_filter.pl
+-rwxrwxr-x  1    339 ubuntu    3351 Feb 24  2017 lipm_bed_split_by_sequence.pl
+-rwxrwxr-x  1    339 ubuntu   26402 Feb 24  2017 lipm_bed_to_expr.pl
+-rwxrwxr-x  1    339 ubuntu    6591 Feb 24  2017 lipm_bed_to_gff3.pl
+-rwxrwxr-x  1    339 ubuntu    4284 Feb 24  2017 lipm_dbprot_remove_repbase.pl
+-rwxrwxr-x  1    339 ubuntu    1600 Feb 24  2017 lipm_fasta2overlappingwins.pl
+-rwxrwxr-x  1    339 ubuntu   15028 Feb 24  2017 lipm_fasta2tree.pl
+-rwxrwxr-x  1    339 ubuntu   10965 Feb 24  2017 lipm_fastafilter.pl
+-rwxrwxr-x  1    339 ubuntu    3700 Feb 24  2017 lipm_fastasplitter.pl
+-rwxrwxr-x  1    339 ubuntu   18852 Feb 24  2017 lipm_genome_statistics.pl
+-rwxrwxr-x  1    339 ubuntu   12125 Feb 24  2017 lipm_m8_to_gff3.pl
+-rwxrwxr-x  1    339 ubuntu    5885 Feb 24  2017 lipm_m8tom8plus.pl
+-rwxrwxr-x  1    339 ubuntu    7770 Feb 24  2017 lipm_N50.pl
+-rwxrwxr-x  1    339 ubuntu 1047496 Feb 24  2017 lipm_nrdb
+-rwxrwxr-x  1    339 ubuntu    1172 Feb 24  2017 lipm_smp.pl
+-rwxrwxr-x  1    339 ubuntu   13886 Feb 24  2017 lipm_transfer_gff3_attributes.pl
+-rwxrwxr-x  1    339 ubuntu   10551 Feb 24  2017 lipm_wig_to_expr.pl
+-rwxrwxr-x  1    339 ubuntu    9792 Feb 24  2017 MapWithBlast.pl
+lrwxrwxrwx  1 root   root        18 Aug 27 15:14 ncbi-blast -> ncbi-blast-2.2.31+
+drwxr-xr-x  4  11236  13030    4096 Jun  2  2015 ncbi-blast-2.2.31+
+lrwxrwxrwx  1    339 ubuntu      13 Feb 24  2017 paraloop -> paraloop-1.3/
+drwxrwxr-x  7    339 ubuntu    4096 Feb 24  2017 paraloop-1.3
+lrwxrwxrwx  1 root   root         9 Aug 27 15:22 red -> redUnix64
+drwxr-x---  2  10194  10194    4096 Jun 18  2015 redUnix64
+-rwxr-xr-x  1   2314 cdrom        0 Aug 27 15:22 rnammer
+-rw-r--r--  1 root   root         0 Feb  5  2015 rnammer-1.2.src.tar.Z
+-rwxr-xr-x  1   2314 cdrom     8849 Aug 27 15:22 rnammere
+drwxr-xr-x  4 root   root      4096 Aug 27 15:10 share
+lrwxrwxrwx  1    339 ubuntu      17 Feb 24  2017 tRNAscan-SE -> tRNAscan-SE-1.3.1
+drwxr-x---  5   2841 users     4096 Aug 27 15:08 tRNAscan-SE-1.3.1
+-rw-r--r--  1 root   root    740960 Jun 16 07:54 tRNAscan-SE.tar.gz
+lrwxrwxrwx  1 root   root        24 Aug 27 15:22 usearch -> usearch9.2.64_i86linux32
+-rwxr-xr-x  1 root   root         0 Aug 27 15:22 usearch9.2.64_i86linux32
+-rwxr-xr-x  1   2314 cdrom        0 Feb  6  2007 xml2fsa
+-rwxr-xr-x  1   2314 cdrom        0 May 22  2007 xml2gff
+     # rm rnammer
+     # mv rnammere rnammer
+```
+
+=>The value of the parameter prg_usearch is >/usr/bin/egnep-1.4/bin/ext/usearch< which is not a name of an existing and non empty file at /usr/bin/egnep-1.4/bin/int/egn-euk.pl line 2307.
+Command exited with non-zero status 25
+
+    scp sidibebocs@cc2-login.cirad.fr:/homedir/sidibebocs/work/ganoderma/egnep-1.4/bin/ext/usearch9.2.64_i86linux32 .
+
+### 4) Empty result file?
+
+```bash
+# more pipeline.txt 
+nohup: ignoring input
+################################################################################
+################################################################################
+# /usr/bin/egnep-1.4/bin/int/egn-euk.pl --indir /root/input_dir/ --outdir /root/output_dir/ --cfg /root/bank_tair/egnep-test.cfg --workingdir /root/work_dir/
+# EuGene Pipeline EUK - version 1.4
+# EUGENEDIR /usr/bin/eugene-4.2a
+# EGNEP /usr/bin/egnep-1.4
+# Log file /root/work_dir/logger.1535964229.7865.txt
+################################################################################
+################################################################################
+
+Create tree.....................................................................started
+Create tree.....................................................................done
+#########################  Protein database cleaning  ##########################
+#####################  Protein sequence similarity search  #####################
+BlastX uniprot-thaliana_swiss2.fasta uniprot-thaliana_trembl2.fasta.............started
+  BLASTX PARAMETERS=-outfmt 6 -evalue 0.01 -gapopen 9 -gapextend 2 -max_target_seqs 500000 -max_intron_length 15000  -seg yes
+  UBLAST PARAMETERS=-threads 8 -evalue 1 -lopen 9 -lext 2 -accel 1
+/usr/bin/egnep-1.4/bin/ext/gmap/bin/gmap_build -d sequences -D /root/work_dir/db/GMAP_INDEX /root/work_dir/sequences 2> /root/work_dir/db/GMAP_INDEX/gmap_idx.7865.stde
+BlastX uniprot-thaliana_swiss2.fasta uniprot-thaliana_trembl2.fasta.............done
+###########################  Transcriptome mapping  ############################
+Gmap TAIR_est2.fasta............................................................started
+  PARAMETERS=-n0 -B 5 -t 8 -L 100000 --min-intronlength=35 -K 25000 --trim-end-exons=25 
+  FILTERS=EST length percentage > 50, identity percentage > 95
+Gmap TAIR_est2.fasta............................................................done
+#############################  IMM model building  #############################
+Build IMM models................................................................started
+    BlastX TAIR_est2.fasta.filterlen300 uniprot-thaliana_swiss2.fasta...........started
+      PARAMETERS=-outfmt 6 -evalue 0.01 -gapopen 9 -gapextend 2 -max_target_seqs 500000 -max_intron_length 15000  -seg yes
+    BlastX TAIR_est2.fasta.filterlen300 uniprot-thaliana_swiss2.fasta...........done
+    BLASTX FILTERS= HSP_length > 100 AA, identity percentage > 50, e-value > 0.0001
+    Gmap TAIR_est2.fasta.filterlen300...........................................started
+      PARAMETERS=-n0 -B 5 -t 8 -L 100000 --min-intronlength=35 -K 25000 --trim-end-exons=25 
+      FILTERS=EST length percentage > 95, identity percentage > 95
+ERROR: no data to train eugene IMM (because no result for mapping of the reference transcriptome to the genomic sequence): choose an other reference transcriptome and launch again.
+    Gmap TAIR_est2.fasta.filterlen300...........................................done
+```
+
+## EGNEP kill
+You know the process identifier (PID = 26448)
+     # nohup $EGNEP/bin/int/egn-euk.pl --no_red --indir /root/input_dir/ --outdir /root/output_dir/ --cfg /root/bank_tair/egnep-test.cfg --workingdir /root/work_dir >& pipeline.txt &
+[1] 26448
+
+You can see all the subprocesses
+```bash
+ ps -edf | grep egn
+root      4507 26367  0 16:11 pts/0    00:00:00 grep --color=auto egn
+root     26448 26367  0 15:47 pts/0    00:00:01 /usr/bin/perl /usr/bin/egnep-1.4/bin/int/egn-euk.pl --no_red --indir /root/input_dir/ --outdir /root/output_dir/ --cfg /root/bank_tair/egnep-test.cfg --workingdir /root/work_dir
+root     31805 26697  0 15:55 pts/0    00:00:00 /usr/bin/perl /usr/bin/egnep-1.4/bin/int/get_BlastX.pl --sequence /root/work_dir/0001/Chr1/Chr1 --cfg /root/bank_tair/egnep-test.cfg --db /root/work_dir/db/uniprot-thaliana_trembl2.fasta --outfile /root/work_dir/0001/Chr1/Chr1.blast2 --workingdir /root/work_dir/0001/Chr1/work.1536421660.26448/
+root     31806 31805  0 15:55 pts/0    00:00:00 /usr/bin/perl /usr/bin/egnep-1.4/bin/ext/MapWithBlast.pl --sequence /root/work_dir/0001/Chr1/Chr1 --db /root/work_dir/db/uniprot-thaliana_trembl2.fasta --output /root/work_dir/0001/Chr1/Chr1.blast2 --workingdir /root/work_dir/0001/Chr1/work.1536421660.26448/ --cfg /root/bank_tair/egnep-test.cfg
+root     31807 31806  0 15:55 pts/0    00:00:00 sh -c export PARALOOP=/usr/bin/egnep-1.4/bin/ext/paraloop ; /usr/bin/egnep-1.4/bin/ext/paraloop/bin/paraloop.pl --clean --wait --ncpus=7 --interleaved --program=Shell --input /root/work_dir/0001/Chr1/work.1536421660.26448//BlastX.31806.1536422142/Chr1_cmd.31806.1536422142 --output /root/work_dir/0001/Chr1/work.1536421660.26448//BlastX.31806.1536422142/Chr1_cmd.31806.1536422142.output  --clean 
+root     31808 31807  0 15:55 pts/0    00:00:00 /usr/bin/perl /usr/bin/egnep-1.4/bin/ext/paraloop/bin/paraloop.pl --clean --wait --ncpus=7 --interleaved --program=Shell --input /root/work_dir/0001/Chr1/work.1536421660.26448//BlastX.31806.1536422142/Chr1_cmd.31806.1536422142 --output /root/work_dir/0001/Chr1/work.1536421660.26448//BlastX.31806.1536422142/Chr1_cmd.31806.1536422142.output --clean
+```
+You need to kill at least
+
+     # kill -9 26448
+     # kill -9 26697
+Before rerunning 
+
+     # rm pipeline.txt 
+     # rm -fr work_dir
+     # mkdir work_dir
diff --git a/_pages/annotation/IFBcloud/create_IFB_cloud_user_account.md b/_pages/annotation/IFBcloud/create_IFB_cloud_user_account.md
new file mode 100644
index 00000000..86242c76
--- /dev/null
+++ b/_pages/annotation/IFBcloud/create_IFB_cloud_user_account.md
@@ -0,0 +1,72 @@
+# How to create an IFB cloud user account
+
+**************************
+**Author(s)**: Stéphanie Bocs, Laurent Bouri, Jacques Dainat
+
+**Date**: 15/09/2018
+
+**Keywords**: IFB cloud, user, account
+
+**Description**: Explanation how create an account on the IFB cloud
+**********
+
+<!-- TOC depthFrom:2 depthTo:2 withLinks:1 updateOnSave:1 orderedList:0 -->
+
+- [IFB cloud user account](#ifb-cloud-user-account)
+- [IFB cloud user ssh-key](#ifb-cloud-user-ssh-key)
+
+<!-- /TOC -->
+
+## IFB cloud user account
+
+### 1) If your institute is not listed in Edugain then ask for the creation of local account fill the form
+
+https://biosphere.france-bioinformatique.fr/cloudweb_account/creation/
+
+![Excel10.3_IFBcloud_01_account_create](https://gitlab.southgreen.fr/excelerate/southgreen10.3/uploads/e74b4c9956310c1c1de683e367d81f70/Excel10.3_IFBcloud_01_account_create.png)
+
+### 2) Connect to your local account
+
+https://biosphere.france-bioinformatique.fr/cloudweb/login/?next=/cloud/
+![Excel10.3_IFBcloud_02_account_connect](https://gitlab.southgreen.fr/excelerate/southgreen10.3/uploads/05d8eed214a4837829a7c543cd6cca0b/Excel10.3_IFBcloud_02_account_connect.png)
+
+## IFB cloud user ssh-key
+
+### 1) Create your ssh key from your personnal computer 
+
+SSH keys serve as a means of identifying yourself to an SSH server using public-key cryptography and challenge-response authentication. One immediate advantage this method has over traditional password authentication is that you can be authenticated by the server without ever having to send your password over the network. Anyone eavesdropping on your connection will not be able to intercept and crack your password because it is never actually transmitted. 
+
+Execute the command ssh-keygen, for instance, on a terminal of Mac OS X personnal computer
+```bash
+$ ssh-keygen
+Generating public/private rsa key pair.
+Enter file in which to save the key (/Users/SIDIBEBOCS/.ssh/id_rsa): 
+Enter passphrase (empty for no passphrase): 
+Enter same passphrase again: 
+Your identification has been saved in /Users/SIDIBEBOCS/.ssh/id_rsa.
+Your public key has been saved in /Users/SIDIBEBOCS/.ssh/id_rsa.pub.
+The key fingerprint is:
+SHA256:Kq12lZ67eI7V3lKK2vdZpe09siG9rcM/v8ua2uaCgwk SIDIBEBOCS@SIDIBEB_ST-J058
+The key's randomart image is:
++---[RSA 2048]----+
+|                 |
+|                 |
+|                 |
+|                 |
+|        S.      .|
+|     E .o.  o  + |
+|    . +o+oo+.oo .|
+|    .o.B=++ooB*+.|
+|   ...++=+o+OOB*X|
++----[SHA256]-----+
+```
+A id_rsa.pub file has been created.
+
+### 2) Copy / paste the public ssh key to your IFB cloud local account
+
+     nedit /Users/SIDIBEBOCS/.ssh/id_rsa.pub &
+Copy its content into the public key field of your IFB cloud personnal account
+
+<img src="/excelerate/southgreen10.3/uploads/bc983cabded1721711c3239af0a3c6bf/Excel10.3_IFBcloud_03_ssh-key_copy.png"  width="800">
+
+In case of problem write to support@france-bioinformatique.fr
\ No newline at end of file
diff --git a/_pages/annotation/IFBcloud/use_IFB_cloud_appliance.md b/_pages/annotation/IFBcloud/use_IFB_cloud_appliance.md
new file mode 100644
index 00000000..52a54f71
--- /dev/null
+++ b/_pages/annotation/IFBcloud/use_IFB_cloud_appliance.md
@@ -0,0 +1,82 @@
+# How to run an IFB cloud appliance
+
+**************************
+**Author(s)**: Stéphanie Bocs, Laurent Bouri, Jacques Dainat
+
+**Date**: 15/09/2018
+
+**Keywords**: appliance, run, use, IFB cloud
+
+**Description**: Explanation how to run and use an IFB cloud appliance
+**********
+
+<!-- TOC depthFrom:2 depthTo:2 withLinks:1 updateOnSave:1 orderedList:0 -->
+
+- [IFB cloud appliance start](#ifb-cloud-appliance-start)
+- [IFB cloud appliance connection](#ifb-cloud-appliance-connection)
+
+<!-- /TOC -->
+
+## Prerequisite
+
+1. You need an account on the IFB could. If you don't have any please refer to the following documentation:
+[How to create an account on the IFB cloud](create_IFB_cloud_user_account)
+
+## IFB cloud appliance start
+
+### 1) Look for your appliance
+
+https://biosphere.france-bioinformatique.fr/catalogue/
+![Excel10.3_IFBcloud_04_rainbio_catalog_search](https://gitlab.southgreen.fr/excelerate/southgreen10.3/uploads/6c474336f757d0f24397977ba2198052/Excel10.3_IFBcloud_04_rainbio_catalog_search.png)
+
+### 2) Configure your VM with the adapted size
+
+Click on advanced deployment then choose the corresponding amount of CPU and RAM needed for your purpose.
+![Excel10.3_IFBcloud_05_eugene_appli_config](https://gitlab.southgreen.fr/excelerate/southgreen10.3/uploads/b5c83c88a60da4fd8faf0bf6a2fc025c/Excel10.3_IFBcloud_05_eugene_appli_config.png)
+
+
+## IFB cloud appliance connection
+
+### 1) Look for your VM
+
+Click on myVM tab, wait for the deployment to finish corectly (green light), then click on the interrogation point in order to obtain the IP address of your VM 
+
+https://biosphere.france-bioinformatique.fr/cloud/
+![Excel10.3_IFBcloud_06_eugene_appli_myVM](https://gitlab.southgreen.fr/excelerate/southgreen10.3/uploads/5924afd5ad276f9437c5029cabcb1d0f/Excel10.3_IFBcloud_06_eugene_appli_myVM.png)
+
+### 2) Connect to your VM
+```bash
+SIDIBEB_ST-J058:~ SIDIBEBOCS$ ssh -Y root@134.158.247.40
+Welcome to Ubuntu 16.04.3 LTS (GNU/Linux 4.4.0-104-generic x86_64)
+
+ * Documentation:  https://help.ubuntu.com
+ * Management:     https://landscape.canonical.com
+ * Support:        https://ubuntu.com/advantage
+
+  Get cloud support with Ubuntu Advantage Cloud Guest:
+    http://www.ubuntu.com/business/services/cloud
+
+75 packages can be updated.
+1 update is a security update.
+
+*** System restart required ***
+
+First, make sure you are root user (sudo su)
+
+Then, read the readme file ReadmeEugen.txt and ReadmeBUSCO.txt for more details on running eugen-EP and BUSCO (/root)
+
+You will find sequence data to try Eugene-EP, located at /root
+
+If you need to launch myGenomeBrowser, run the script script_myGenomeBrowser.sh (/root) (login/password generated)
+
+Then, type 'firefox &' to start the firefox browser (You must have used the -XY arguments in your ssh connection)
+
+Finally, enter the following URL in firefox to connect to the MyGenomeBrowser portal: http://localhost/myGenomeBrowser
+
+And use the login and password provided in the terminal to log in to myGenomeBrowser
+
+Last login: Fri Sep  7 15:18:07 2018 from 195.221.174.11
+root@machine1a957191-dcc3-4d5e-83d7-e97d29f17266:~# ls
+bank_tair  bank_tair.zip  input_dir  output_dir  ReadmeBusco.txt  ReadmeEugen.txt  script_myGenomeBrowser.sh  work_dir
+```
+In case of problem write to support@france-bioinformatique.fr
\ No newline at end of file
diff --git a/_pages/annotation/MAKER/StructuralAnnotation_mtp.md b/_pages/annotation/MAKER/StructuralAnnotation_mtp.md
new file mode 100644
index 00000000..37c8139a
--- /dev/null
+++ b/_pages/annotation/MAKER/StructuralAnnotation_mtp.md
@@ -0,0 +1,330 @@
+---
+title: Assembly and Annotation Course - Montpellier
+author: Jacques Dainat
+date: 14/09/2018
+---
+
+## Foreword:
+
+We will in this practical session use data from Arabidopsis thaliana, as that is one of the currently best annotated plant organisms and there is plenty of high quality data available. However, working on eukaryotes can be time consuming. Even a small plant genome like Arabidopsis thaliana (135 Mpb) would take too long to run within the time we have for this course. Thus to be sure to perform the practicals in good conditions, we will use the smallest chromosome, (chromosome 4 - 18 Mbp). Nevertheless, this chromosome could take several hours to be proceessed by MAKER on 8 cpu, so in order to work in a managable time, we decided to use only 1 Mbp of the chromosome 4. We will call it `genome` all along the excercices.
+An annotation project requires numerous tools and dependencies, which can take easily many days to install for a neophyte. For your convenience and in order to focus on the art of the ANNOTATION most of the tools are ready to use.
+
+## First of all
+
+### Prepare your VM
+
+Before going into the exercises below you need to connect to your Unix virtual machine (VM) following the instruction we provided you (in a terminal: ssh -Y -p <port> <username>@<host>).
+Once connected create a new folder for this exercise:
+```bash
+cd ~
+mkdir annotation
+cd annotation
+mkdir maker
+cd maker
+cp /home/data/data_lsoler/functional_annotation/data/genome.fa .
+export PATH=/home/data/opt-byod/GAAS/annotation/:/home/data/opt-byod/GAAS/annotation/Tools/bin/:$PATH
+```
+
+
+### Prepare your aplliance
+
+Once done you will to launch a second virtual machine (Yes twice as much fun !) in a second terminal. This second VM is called `appliance MAKER` and will be used to launch the MAKER annotation.
+
+[1) Create a user account on the IFB cloud (if not already done)](../IFBcloud/create_IFB_cloud_user_account.md)
+
+[ Launch a MAKER appliance on the IFB cloud](../IFBcloud/use_IFB_cloud_appliance.md)
+
+Part 1 - Check of your Assembly (on VM)
+---------------------------------------
+
+Before starting an annotation project, we need to carefully inspect the assembly to identify potential problems before running expensive computes.
+You can look at i) the Fragmentation (N50, N90, how many short contigs); ii) the Sanity of the fasta file (Presence of Ns, presence of ambiguous nucleotides, presence of lowercase nucleotides, single line sequences vs multiline sequences); iii) completeness using BUSCO; iv) presence of organelles; v) Others (GC content, How distant the investigated species is from the others annotated species available).
+The two next exercices will perform some of these checks.
+
+### 1.1 Checking the gene space of your assembly
+
+BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness. Genes that make up the BUSCO sets for each major lineage are selected from orthologous groups with genes present as single-copy orthologs in at least 90% of the species.
+
+***Note:*** In a real-world scenario, this step come first and foremost. Indeed, if the result is under your expectation you might be required to enhance your assembly before to go further.
+
+**_Exercise 1_ - BUSCO -:**
+
+Good news, you don't have to do anything here. As you already learned how to use busco during the assembly part of the course. Let's jump directly to the next step.
+
+
+### 1.2 Various Check of your Assembly (on VM)
+
+**_Exercise 2_ :**
+Launching the following script will provide you some useful information.
+
+```bash
+fasta_statisticsAndPlot.pl -f genome.fa
+```
+
+If you don't see any peculiarities, you can then decide to go forward and start to perform your first wonderful annotation.
+
+Part 2 - Understand MAKER and its control files (on appliance)
+---------------------------------------
+
+## Overview
+
+**MAKER** is a computational pipeline to automatically generate annotations from a range of input data - including proteins, ESTs, RNA-seq transcripts and ab-initio gene predictions. During this exercise, you will learn how to use Maker with different forms of input data, and how to judge the quality of the resulting annotations.
+
+The Maker pipeline can work with any combination of the following data sets:
+
+* Proteins from the same species or related species  
+
+* Proteins from more distantly related organisms (e.g. Uniprot/Swissprot)  
+
+* Transcriptome sequences from the same species or very closely related species  
+
+* Ab-initio predictions from one or more tools (directly supported are: Augustus, Snap, GeneMark, Fgenesh)  
+
+At minimum, most annotation projects will run with a protein data set, possibly complemented by some RNA-seq data. Popular examples of this are most of the traditional model systems, including human. However, a potential shortcoming of such approaches is that the comprehensiveness of the annotation depends directly on the input data. This can become a problem if our genome of interest is taxonomically distant to well-sequenced taxonomic groups so that only few protein matches can be found. Likewise, not all genes will be expressed at all times, making the generation of a comprehensive RNA-seq data set for annotation challenging.
+
+We will therefore first run our annotation project in the traditional way, with proteins and ESTs, and then repeat the process with a well-trained ab-initio gene predictor. You can then compare the output to get an idea of how crucial the use of a gene predictor is. However, before we get our hands dirty, we need to understand Maker a little better...
+
+Maker strings together a range of different tools into a complex pipeline (e.g. blast, exonerate, repeatmasker, augustus...), fortunately all its various dependencies have been already installed for you. 
+
+
+## Understanding Makers control files (on appliance)
+
+Check that everything is running smoothly by creating the MAKER config files:
+
+```bash
+cd ~/annotation/maker
+mkdir maker_evidence
+cd maker_evidence
+maker -CTL
+ls -l
+```
+
+Makers behaviour and information on input data are specified in one of three control files. These are:
+
+- maker_opts.ctl  
+- maker_bopts.ctl  
+- maker_exe.ctl
+
+What are these files for?
+
+'maker_exe.ctl' holds information on the location of the various binaries required by Maker (including Blast, Repeatmasker etc). Normally, all information in this file will be extracted from $PATH, so if everything is set up correctly, you will never have to look into this file.
+
+Next, 'maker_bopts.ctl' provides access to a number of settings that control the behaviour of evidence aligners (blast, exonerate). The default settings will usually be fine, but if you want to try to annotate species with greater taxonomic distance to well-sequenced species, it may become necessary to decrease stringency of the e.g. blast alignments.
+
+Finally, 'maker_opts.ctl' holds information on the location of input files and some of the parameters controlling the decision making during the gene building.
+
+Part 3 - Create an evidence-based annotation with MAKER (on appliance)
+---------------------------------------
+
+To save you some time, you don't need to seek for evidence data, we provide you proteins from uniprot as well as EST from NCBI.
+
+### Overview
+
+The first run of Maker will be done without ab-initio predictions. What are your expectations for the resulting gene build? In essence, we are attempting a purely evidence-based annotation, where the best protein- and EST-alignments are chosen to build the most likely gene models. The purpose of an evidence-based annotation is simple. Basically, you may try to annotate an organism where no usable ab-initio model is available. The evidence-based annotation can then be used to create a set of genes on which a new model could be trained on (using e.g. Snap or Augustus). Selection of genes for training can be based on the annotation edit distance (AED score), which says something about how great the distance between a gene model and the evidence alignments is. A score of 0.0 would essentially say that the final model is in perfect agreement with the evidence.
+
+Let's do this step-by-step:
+
+## Prepare the input data
+
+Link the raw computes you want to use into your folder. The files you will need are:
+
+- the gff file of the pre-computed repeats (coordinates of repeatmasked regions)
+
+```bash
+ln -s ~/annotation_course/data/raw_computes/repeatmasker.gff
+```
+
+In addition, you will also need the genome sequence.
+```bash
+ln -s ~/annotation_course/data/genome/genome.fa
+```
+Then you will also need EST previously align (gff format) and protein fasta file:  
+```bash
+ln -s ~/annotation_course/data/evidence/est2genome.gff 
+ln -s ~/annotation_course/data/evidence/proteins.fa
+```
+
+/!\\ Always check that the gff files you provides as protein or EST contains   match / match_part (gff alignment type ) feature types rather than genes/transcripts (gff annotation type) otherwise MAKER will not use the contained data properly. Here all the data are fine.
+
+You should now have 1 repeat file, 1 EST file, 1 protein file and the genome sequence in fasta format in the working directory. 
+
+For Maker to use this information, we need creating the three config files, typing this command:
+```bash
+maker -CTL
+```
+
+You can leave the two files controlling external software behaviors untouched. In the actual maker options file called **maker_opts.ctl**, we need to provide:
+
+- name of the genome sequence (genome=)
+- name of the 'EST' file in fasta format  (est_gff=)
+- name of the 'Protein' set file(s) (protein=)
+- name of the repeatmasker file (rm_gff=) 
+
+You can list multiple files in one field by separating their names by a **comma** ','.
+
+This time, we do not specify a reference species to be used by augustus, which will disable ab-initio gene finding. Instead we set:
+  
+  <i>protein2genome=1</i>  
+  <i>est2genome=1</i>
+
+This will enable gene building directly from the evidence alignments.
+
+To edit the **maker_opts.ctl** file you can use the nano text editor:
+```bash
+nano maker_opts.ctl
+```
+
+Before running MAKER you can check you have modified the maker_opts.ctl file properly [here](practical2_supl_maker.md).<br/>
+/!\ Be sure to have deactivated the parameters **model\_org= #** and **repeat\_protein= #** to avoid the heavy work of repeatmasker.
+
+## Run Maker
+
+If your maker\_opts.ctl is configured correctly, you should be able to run maker:
+```
+mpiexec -n 8 maker
+```
+This will start Maker on 8 cores, if everything is configured correctly.
+This will take a little while and process a lot of output to the screen. Luckily, much of the heavy work - such as repeat masking - are already done, so the total running time is quite manageable, even on a small number of cores.
+
+## While Maker is running (1):
+
+/home/data/opt-byod/GAAS/annotation/BILS/Handler/Benchmark/gff_ben
+
+## Inspect the output
+
+[Here you can find details about the MAKER output.](inspect_the_output.md)
+
+## Compile the output
+
+Once Maker is finished, you need gathering all the outputs in some usable form.
+You have two options: copy select files by hand to wherever you want them; or you can use scripts that do the job for you.
+
+MAKER comes with fasta_merge and gff3_merge scripts but we promote to use the script called 'maker\_merge\_outputs\_from\_datastore' from the [GAAS](https://github.com/NBISweden/GAAS) git repository already include in your VM (not with the appliance). Consequently you need to copy (rsync or scp) the genome.maker.output folder on your VM first. Then, in your VM, if you are in the same folder where genome.maker.output is located you should be able to use this command:
+```bash
+maker_merge_outputs_from_datastore.pl --output maker_output_processed_evidence
+```
+We have specified a name for the output directory since we will be creating more than one annotation and need to be able to tell them apart.  
+
+[Here you can find details about the MAKER result.](inspect_the_result.md)
+
+The **maker.gff** is the result to keep from this analysis. 
+
+=> You could sym-link the maker.gff file to another folder called e.g. maker\_results, so everything is in the same place in the end. Just make sure to call the link something other than maker.gff (e.g maker_evidence.gff), since any maker output will be called like that.
+
+
+## Inspect the gene models
+
+To get some statistics of your annotation you could launch :
+```bash
+gff3_sp_statistics.pl --gff maker_output_processed_abinitio/gff_by_type/maker.gff
+```
+
+We could now also visualise the annotation in a genome browser (IGV).
+
+
+Part 4 - Create an abinitio evidence-driven annotation with MAKER
+---------------------------------------
+
+The recommended way of running Maker is in combination with one or more ab-initio profile models. Maker natively supports input from several tools, including augustus, snap and genemark. The choice of tool depends a bit on the organism that you are annotating - for example, GeneMark-ES is mostly recommended for fungi, whereas augustus and snap have a more general use.
+
+The biggest problem with ab-initio models is the process of training them. It is usually recommended to have somewhere around 500-1000 curated gene models for this purpose. Naturally, this is a bit of a contradiction for a not-yet annotated genome.
+
+However, if one or more good ab-initio profiles are available, they can potentially greatly enhance the quality of an annotation by filling in the blanks left by missing evidence. Interestingly, Maker even works with ab-initio profiles from somewhat distantly related species since it can create so-called hints from the evidence alignments, which the gene predictor can take into account to fine-tune the predictions.
+
+Usually when no close ab-initio profile exists for the investigated species, we use the first round of annotation (evidence based) to create one. We first filter the best gene models from this annotation, which are used then to train the abinitio tools of our choice.
+
+In order to compare the performance of Maker with and without ab-initio predictions in a real-world scenario, we have first run a gene build without ab-initio predictions. Now, we run a similar analysis but enable ab-initio predictions through augustus.
+
+## Prepare the input data
+
+No need to re-compute the mapping/alignment of the different lines of evidence. Indeed, this time consuming task has already been performed during the previous round of annotation (evidence based). So, we will use the corresponding gff files previously produced by MAKER.
+
+Link the gff files you want to use into your folder:
+
+ - repeatmasker.gff (already present)
+ - genome.fa (already present) 
+ - est2genome.gff (already present) 
+ - protein2genome.gff 
+
+```bash
+ln -s maker_output_processed_evidence/gff_by_type/protein2genome.gff
+```
+
+This time, we do specify a reference species to be used by augustus, which will enable ab-initio gene finding.
+To see which species have already a hmm profile included in augustus launch:
+```bash
+augustus --species=help
+```
+Select the appropriate species and inform MAKER in the maker_opt.ctl file (replace **my_species** by your choice:
+
+*augustus\_species=**my_species*** #Augustus gene prediction species model  (this is where you can call the database you trained for augustus)
+...  
+<i>protein2genome=0</i>  
+<i>est2genome=0</i>
+
+If you want to keep abinitio prediction not supported by any evidences you can as well activate the keep_pred option:
+
+*keep_preds=1*
+
+/!\\ keep_preds is not recommended for plant genomes.
+
+With these settings, Maker will run augustus to predict gene loci, but inform these predictions with information from the protein and est alignments.
+
+Before running MAKER you can check you have modified the maker_opts.ctl file properly [here](practical2_supl3_maker.md).
+
+## Run Maker with ab-initio predictions
+
+With everything configured, run Maker as you did for the previous analysis:
+```bash
+mpiexec -n 8 maker
+```
+
+## While Maker is running (2):
+
+## Compile the output
+
+When Maker has finished, copy past the genome.maker.output on your VM and then compile the output:
+```bash
+maker_merge_outputs_from_datastore.pl --output maker_output_processed_abinitio 
+```
+And again, it is probably best to link the resulting output (maker.gff) to a result folder (the same as defined in the previous exercise e.g. maker\_results), under a descriptive name (e.g maker_abinitio.gff).
+
+## Inspect the gene models
+
+To get some statistics of your annotation you could launch :
+```
+gff3_sp_statistics.pl --gff maker_output_processed_abinitio/gff_by_type/maker.gff
+```
+
+**Question:** Do you have more or less gene models compare to the evidence-based annotation ?
+
+We could now also visualise the annotation in a genome browser.
+
+
+Part 5 - Complete the annotation
+---------------------------------------
+
+You prabably have now the two maker annotation (maker_evidence.gff and maker_abinitio.gff) in one folder. If not create a folder with a link to those two annotation. Now move into this folder.
+We will take one of these annotation as reference, and the other as target. We will complement the reference annotation with loci that are annotated in the target but absent in the reference like that:
+
+```bash
+./gff3_sp_complement_annotations.pl --ref annotation_ref.gff --add=target.gff --out=final_annotation.gff
+```
+
+Get some statistics of your new annotation:
+```
+gff3_sp_statistics.pl --gff final_annotation.gff
+```
+
+**Question:** How many genes did you succed to catch from your target annotation ?
+
+**Remark**: Launchung BUSCO on the proteins resulting of your annotation and comparing the result against the BUSCO you should have launched on the assembly will provide you nice hints about the quality of your annotation. In case of a huge drop of the `complete BUSCOs`, something went probably wrong during your annotation (paramters ? Hints provided ? hmm profile use ?).
+
+
+## Closing remarks
+
+This concludes the gene building part. We have learned how to use the Maker annotation pipeline and have created gene builds with and without ab-initio predictions. We showed you that the running of an annotation pipeline like Maker is not very hard. Actually the complicated work comes after. How to we best inspect the gene builds? Count features? Visualize it? Most importantly, what steps do we need to take to create a 'finished' annotation that we can use for scientific analyses ? 
+In oder to assess the quality of an annotation the use of simple statistics like done here or BUSCO as mentioned several times are good choices. On top of that, an inspection of the annotation in genome browser is really important. We will approach this in another session (Manual curation). But assessing the annotation quality is in any case an easy task.
+With that being said, the structural annotation was just a step. Now you will have to make an attempt at functional inference for the predicted gene models. Thus will be approach in another session (functional curation).
+
+ Keep in mind that the exercices have been modeled to fit in the provided time. Many other important aspects of the structural annotation work haven't been approached (e.g Gathering evidence data for annotation (Protein, EST and RNA-seq data), Assembling transcripts based on RNA-seq data, how to train ab-initio tools, Comparing and evaluating annotations, etc).
\ No newline at end of file
diff --git a/_pages/annotation/MAKER/inspect_the_output.md b/_pages/annotation/MAKER/inspect_the_output.md
new file mode 100644
index 00000000..0391404e
--- /dev/null
+++ b/_pages/annotation/MAKER/inspect_the_output.md
@@ -0,0 +1,37 @@
+## Inspect the output
+
+### Finding your way around
+
+By default, Maker will write the output of its different analyses into a folder named:
+
+**&lt;name\_of\_genome\_fasta&gt;.maker.output**
+
+In our case:
+
+**genome.maker.output**
+
+Within the main output directory, Maker keeps a copy of the config files, a database (here: 4.db), directories for the blast databases created from your evidence data and a file called genome\_master\_datastore\_index.log.
+
+Out of these files, only the genome\_master\_datastore\_index is really interesting to us. It includes a log of all the contigs included in the genome fasta file - together with their processing status (ideally: FINISHED) and the location of the output files. Since Maker can technically run in parallel on a large number of contigs, it creates separate folders for each of these input data. For larger genomes, this can generate a very deep and confusing folder tree. The genome\_master\_datastore\_index.log helps you make sense of it:
+```bash
+chr4    genome_datastore/27/AC/chr4/    STARTED
+chr4    genome_datastore/27/AC/chr4/    FINISHED
+```
+This meens the sequence **chr4** was started - and finished, with all data (annotation, protein predictions etc) written to the subfolder genome\_datastore/27/AC/chr4/.
+
+If you look into that folder, you will find the finished Maker annotation for this contig.
+```bash
+rw-rw-r- 1 student student 472193 Mar 24 10:16 chr4.gff <br/>
+\*rw-rw-r- 1 student student 3599 Mar 24 10:16 chr4.maker.augustus\_masked.proteins.fasta <br/>
+\*rw-rw-r- 1 student student 10388 Mar 24 10:16 chr4.maker.augustus\_masked.transcripts.fasta  <br/>
+\*rw-rw-r- 1 student student 176 Mar 24 10:16 chr4.maker.non\_overlapping\_ab\_initio.proteins.fasta <br/>
+\*rw-rw-r- 1 student student 328 Mar 24 10:16 chr4.maker.non\_overlapping\_ab\_initio.transcripts.fasta  <br/>
+rw-rw-r- 1 student student 3931 Mar 24 10:16 chr4.maker.proteins.fasta  <br/>
+rw-rw-r- 1 student student 20865 Mar 24 10:16 chr4.maker.transcripts.fasta  <br/>
+rw-rw-r- 1 student student 4248 Mar 24 10:15 run.log  <br/>
+drwxrwsr-x 3 student student 4096 Mar 24 10:16 theVoid.chr4
+```
+
+\* only if an abinitio tool has been activated
+
+The main annotation file is 'chr4.gff' - including both the finished gene models and all the raw compute data. The other files include fasta files for the different sequence features that have been annotated - based on ab-initio predictions through augustus as well as on the finished gene models. The folder 'theVoid' include all the raw computations that Maker has performed to synthesize the evidence into gene models.
\ No newline at end of file
diff --git a/_pages/annotation/MAKER/inspect_the_result.md b/_pages/annotation/MAKER/inspect_the_result.md
new file mode 100644
index 00000000..3044c720
--- /dev/null
+++ b/_pages/annotation/MAKER/inspect_the_result.md
@@ -0,0 +1,49 @@
+## Inspect the result
+
+You have two options now for gathering the output from MAKER in some usable form - copy select files by hand to wherever you want them. Or you can use scripts that do the job for you.
+
+MAKER comes with fasta_merge and gff3_merge scripts but we promote to use the script called 'maker\_merge\_outputs\_from\_datastore' from the [GAAS](https://github.com/NBISweden/GAAS) git repository already include in your VM (not with the appliance). Consequently you need to copy (rsync or scp) the genome.maker.output on your VM. Then if you are in the same folder where genome.maker.output is located you should be able to use this command:
+```bash
+maker_merge_outputs_from_datastore.pl 
+```
+This will create a directory called "**maker_output_processed**" containing:
+
+\-annotations.proteins.fa 
+\-maker_bopts.ctl  
+\-maker_evm.ctl
+\-maker_exe.ctl
+\-maker_opts.ctl
+\-mixup.gff
+\-gff_by_type/  
+
+ - ***mixup.gff* file**  
+
+It's a mix of all the gff tracks produced/handled by maker. It contains the annotation done by maker mixed up with other gff lines like the protein alignments, repeats, etc..
+If you use 'less' to read the annotation file *mixup.gff* ([GFF3 format](http://www.sequenceontology.org/gff3.shtml)), you will see a range of different features:
+```
+##gff-version 3  
+chr4       .       contig  1       1351857 .       .       .       ID=4;Name=4
+chr4       maker   gene    24134   25665   .       +       .       ID=maker-4-exonerate_protein2genome-gene-0.0;Name=maker-4-exonerate_protein2genome-gene-0.0
+chr4       maker   mRNA    24134   25665   917     +       .       ID=maker-4-exonerate_protein2genome-gene-0.0-mRNA-1;Parent=maker-4-exonerate_protein2genome-gene-0.0;Name=maker-4-exonerate_protein2genome-gene-0.0-mRNA-1;_AED=0.09;_eAED=0.09;_QI=0|0.33|0.25|1|0|0|4|44|290
+```
+...
+
+For example, the above lines read:
+
+A new contig is being shown, with the id 'chr4' and a length of 1351857 nucleotides  
+On this contig, a gene feature is located from position 24134 to 25665, on the plus strand and with the id 'maker-4-exonerate\_protein2genome-gene-0.0'. 
+On this contig, belonging to the gene, is located a transcript from position 24134 to 25665, on the plus strand and with the id 'maker-4-exonerate\_protein2genome-gene-0.0-mRNA-1'. It's quality, or AED score, is 0.09 - which means that the evidence alignments are close to be in perfect agreement with the transcript model.
+
+And so on.
+
+ - ***annotations.proteins.fa* file**  
+This file contains the proteins translated from the CDS of gene models predicted.
+
+ - ***maker_\*.ctl* files**
+
+ Those are backups in case you would like to remember in the future how you have used MAKER to get the corresponding results.
+
+ - ***gff_by_type* directory**  
+The different types of information present in the annotation file (mixup.gff) are separated into independent files into the "gff_by_type" directory.This is useful for a number of applications, like visualizing it as separate tracks in a genome browser. Or to compute some intersting numbers from the gene models.
+
+This should contains a bunch of files, including '**maker.gff**' - which contains the actual gene models.
\ No newline at end of file
diff --git a/_pages/annotation/MAKER/practical2_supl3_maker.md b/_pages/annotation/MAKER/practical2_supl3_maker.md
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+
+# Configure the maker_opts.ctl properly for the abinitio evidence-driven annotation:
+
+
+\#-----Genome (these are always required)  
+**genome=genome.fa** #genome sequence (fasta file or fasta embeded in GFF3 file)  
+organism\_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic
+
+...
+
+\#-----EST Evidence (for best results provide a file for at least one) 
+est= #set of ESTs or assembled mRNA-seq in fasta format  
+altest= #EST/cDNA sequence file in fasta format from an alternate organism  
+**est\_gff=est2genome.gff, est_gff_stringtie.gff** #aligned ESTs or mRNA-seq from an external GFF3 file  
+altest\_gff= #aligned ESTs from a closly relate species in GFF3 format
+
+...
+
+\#-----Protein Homology Evidence (for best results provide a file for at least one)  
+**protein=** #protein sequence file in fasta format (i.e. from mutiple oransisms)  
+**protein\_gff=protein2genome.gff** #aligned protein homology evidence from an external GFF3 file
+
+...
+
+\#-----Repeat Masking (leave values blank to skip repeat masking)  
+**model\_org=** #select a model organism for RepBase masking in RepeatMasker  
+rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker   
+**repeat\_protein=** #provide a fasta file of transposable element proteins for RepeatRunner  
+**rm\_gff=repeatmasker.gff** #pre-identified repeat elements from an external GFF3 file  
+prok\_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no  
+softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
+
+...
+
+\#-----Gene Prediction  
+snaphmm= #SNAP HMM file  
+gmhmm= #GeneMark HMM file  
+**augustus\_species=arabidopsis** #Augustus gene prediction species model  
+fgenesh\_par\_file= #FGENESH parameter file  
+pred\_gff= #ab-initio predictions from an external GFF3 file  
+model\_gff= #annotated gene models from an external GFF3 file (annotation pass-through)  
+**est2genome=0** #infer gene predictions directly from ESTs, 1 = yes, 0 = no  
+**protein2genome=0** #infer predictions from protein homology, 1 = yes, 0 = no  
+trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no  
+snoscan\_rrna= #rRNA file to have Snoscan find snoRNAs  
+unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no
+
+...
+**keep_preds=1**
+...
+
+To better understand the different parameters you can have a look [here](http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_control_files_explained) 
diff --git a/_pages/annotation/MAKER/practical2_supl_maker.md b/_pages/annotation/MAKER/practical2_supl_maker.md
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+# Configure your maker project : The maker_opts.ctl file in detail:
+
+ 
+When executing the command "maker -CTL" MAKER creates 3 control files.
+Of these, only **maker_opts.ctl** is of concern to us. Have a look at the following sections and fill in the information as shown:
+
+\#-----Genome (these are always required)  
+genome=**genome.fa** #genome sequence (fasta file or fasta embeded in GFF3 file)  
+organism\_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic
+
+...
+
+\#-----EST Evidence (for best results provide a file for at least one)  
+est= #set of ESTs or assembled mRNA-seq in fasta format  
+altest= #EST/cDNA sequence file in fasta format from an alternate organism  
+**est\_gff=est2genome.gff** #aligned ESTs or mRNA-seq from an external GFF3 file  
+altest\_gff= #aligned ESTs from a closly relate species in GFF3 format
+
+...
+
+\#-----Protein Homology Evidence (for best results provide a file for at least one)  
+**protein=proteins.fa** #protein sequence file in fasta format (i.e. from mutiple oransisms)  
+protein\_gff= #aligned protein homology evidence from an external GFF3 file
+
+...
+
+\#-----Repeat Masking (leave values blank to skip repeat masking)<br/>
+**model\_org=** #select a model organism for RepBase masking in RepeatMasker  
+rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker   
+**repeat\_protein=** #provide a fasta file of transposable element proteins for RepeatRunner  
+rm\_gff=**repeatmasker.gff** #pre-identified repeat elements from an external GFF3 file  
+prok\_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no  
+softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
+
+...
+
+\#-----Gene Prediction  
+snaphmm= #SNAP HMM file  
+gmhmm= #GeneMark HMM file  
+augustus\_species= #Augustus gene prediction species model  
+fgenesh\_par\_file= #FGENESH parameter file  
+pred\_gff= #ab-initio predictions from an external GFF3 file  
+model\_gff= #annotated gene models from an external GFF3 file (annotation pass-through)  
+**est2genome=1** #infer gene predictions directly from ESTs, 1 = yes, 0 = no  
+**protein2genome=1** #infer predictions from protein homology, 1 = yes, 0 = no  
+trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no  
+snoscan\_rrna= #rRNA file to have Snoscan find snoRNAs  
+unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no
+
+To better understand the different parameters you can have a look [here](http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_control_files_explained)