Renamed files. Deleted seqlogo files.

Author: rfarouni

.travis.yml

@@ -2,9 +2,9 @@ language: python
 
 matrix:
     include:
-        - os: linux
-          dist: trusty
-          python: 2.7
+#        - os: linux
+#          dist: trusty
+#          python: 2.7
         - os: linux
           dist: Xenial
           python: 2.7

DOCKER_FILE_HAYSTACK

@@ -10,10 +10,8 @@ FROM ubuntu:16.04
 MAINTAINER Luca Pinello 
 
 RUN apt-get update && apt-get install git wget default-jre python-setuptools python-pip python-dev python-numpy python-scipy python-matplotlib python-pandas python-imaging python-setuptools unzip ghostscript make gcc g++ zlib1g-dev zlib1g -y
-
+RUN pip install weblogo pybedtools tqdm
 RUN pip install haystack_bio --no-use-wheel --verbose
-
-RUN haystack_download_genome hg19
-RUN haystack_download_genome mm9
+RUN haystack_download_genome hg19 --yes
 
 

haystack/external.py

@@ -1224,7 +1224,7 @@ def generate_weblogo(motif_id,meme_filename,output_filename,file_format='png',ti
     seqs2fasta(kmers,tmp)
 
     tmp= "/home/rick/cap.fa"
-    cmd = 'weblogo -F %s  -A dna  -f %s  -o %s  -t "%s"   --errorbars NO  --fineprint "" '%(file_format, tmp, output_filename, title)
+    cmd = 'weblogo -F %s  -A dna  -f %s  -o %s  -t "%s"  --size large --errorbars NO  --fineprint "" '%(file_format, tmp, output_filename, title)
     #print cmd 
     sb.call(cmd,shell=True)