merge devel

Author: nservant

INSTALL

@@ -17,7 +17,10 @@ Dependencies are checked during installation.
 A couple of tools such as bowtie2 and samtools (>1.0) can be automatically installed if not detected.
 Others have to be installed before starting the installation :
 
-- R http://www.r-project.org/
+- R (http://www.r-project.org/) with the following packages
+--- ggplot2 (>2.2.1)
+--- RColorBrewer
+--- grid
 - Python libraries :
 --- bx-python (>=0.5.0) - https://pypi.python.org/pypi/bx-python
 --- numpy (>=1.8.2) - http://www.scipy.org/scipylib/download.html

LOGBOOK

@@ -7,23 +7,25 @@
 ##
 ################################################################################
 
-o Error if sample dir is named 'fastq'
+o Specify a chromosome subsets in the configuration file (to deal with random for instance)
 
-o Add a way to load paired BAM file
+o It seems that recent PE data does not have the same read names ??
 
-o New graph for Dumped pairs (see. Angelo's idea on the forum)
+o Look at issues about good practice installation
 
-o HiCUP compare
+o Support for Python 3
 
-o Assign reads using its 5' end ...
+o error if rerun the analysis twice in the same folder (rawdata link)
 
-o bug in samtools
+o Add a way to load paired BAM file
 
-o look at pull request
+o Could we image to support other mapper ??
 
-o bug in plot using R3.1.2 and ggplot 2.2.1
+o New graph for Dumped pairs (see. Angelo's idea on the forum)
+
+o Assign reads using its 5' end ...
 
-o update qsub in step2 for paralleization per sample
+o update qsub in step2 for parallelization per sample
 
 o EV - update error tracking
 
@@ -35,17 +37,20 @@ o Deal with reads with multiple RS sites ?
 
 o Check the impact of reads ordering in pairs classification
 
-o Update of HiC-Pro for capture-C data
-
-o Think about a docker version of HiC-Pro
-
 
 ################################################################################
 ##
 ## LOGBOOK
 ##
 ################################################################################
 
+##--------------------
+## 22-12-17
+##--------------------
+
+   o New major realease of HiC-Pro is almost ready (2.10.0). Still a few idea of improvments in the todo list !
+
+
 ##--------------------
 ## 21-03-16
 ##--------------------

Makefile

@@ -53,7 +53,7 @@ readstrimming: $(INST_SOURCES)/cutsite_trimming.cpp
 
 ## Build Python lib
 iced: $(INST_SOURCES)/ice_mod
-	(cp $(INST_SOURCES)/ice_mod/iced/scripts/ice ${INST_SCRIPTS}; cd $(INST_SOURCES)/ice_mod/; ${PYTHON_PATH}/python setup.py install --user;)
+	(cp $(INST_SOURCES)/ice_mod/iced/scripts/ice ${INST_SCRIPTS}; cd $(INST_SOURCES)/ice_mod/; ${PYTHON_PATH}/python setup.py install;)
 
 test: config_check
 	@echo ${PYTHON_PATH}

NEWS

@@ -1,3 +1,48 @@
+***********************************
+CHANGES IN VERSION 2.10.0
+
+NEW FEATURES
+
+   o New utility - hicpro2higlass.sh to convert HiC-Pro output into higlass .cool files
+
+   o HiC-Pro is now availabe as a Singularity container !
+
+   o hicpro2juicebox.sh utility now supports alof HiC-Pro format (< 2.7.5)
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+   o N_CPU parameter is now correcly used for the mapping step. R1 and R2 reads are now mapped using N_CPU/2 CPUs
+
+   o add simple script for unit testing 'test-op'
+
+   o udpate R scripts to be compatible with the lastest ggplot2 version (>2.2.1) and fix graphical bugs in quality controls
+
+   o add new checks on input files and configuration files
+
+   o Only provide HindIII annotation files for Mouse and Human as examples.
+
+BUG FIXES
+
+   o Remove the --user option during iced installation
+
+   o R sessions are no longer saved and restored
+
+   o hicpro2fithic - bug fix when no -o option specified 
+
+   o Fix bug to avoid floating values in valid pair positions 
+
+   o Fix bug in order of samtools sort parameter in bowtie_combine.sh
+
+   o Fix bug in output option of makeViewpoints
+
+   o fix bugs in plots of no trans interactions were detected
+
+   o fix bug in split_reads.py when -o is specified
+
+   o fix issue in hicpro2juicebox.sh. The first column was duplicated, and position are now 1-based
+
+   o fix bug in ice_norm.sh when HiC-Pro is run with -s ice_norm option
+
 ***********************************
 CHANGES IN VERSION 2.9.0