Merge branch 'hotfix/2.4.1'

* added a topaht-fusion-post patch, in which the contig name bug #37 is fixed
cancerit · Oct 18, 2019 · e8223cb · e8223cb
2 parents 43dd4fe + 8adce9c
commit e8223cb
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 2.4.1
+
+* added a patched topaht-fusion-post script, in which the contig name bug #37 is fixed
+
 ## 2.4.0
 
 * Revised Dockerfile so that the builder stage is properly used and the image size is reduced. Resolved #28.

diff --git a/Dockerfile b/Dockerfile
@@ -47,6 +47,7 @@ pkg-config \
 zlib1g-dev \
 zip \
 unzip \
+patch \
 libpng-dev \
 python3 python3-dev python3-pip python3-setuptools \
 r-base r-base-dev \
@@ -78,7 +79,7 @@ ENV LC_ALL en_US.UTF-8
 ENV LANG en_US.UTF-8
 
 # build tools from other repos
-ADD build/opt-build.sh build/
+ADD build build/
 RUN bash build/opt-build.sh $OPT
 
 # build the tools in this repo, separate to reduce build time on errors
@@ -90,7 +91,7 @@ FROM ubuntu:16.04
 
 LABEL maintainer="cgphelp@sanger.ac.uk" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="2.4.0" \
+      version="2.4.1" \
       description="cgpRna docker"
 
 # Version of tools that are installed in both stages, make sure they are consistent.

diff --git a/build/opt-build.sh b/build/opt-build.sh
@@ -144,14 +144,17 @@ if [ ! -e $SETUP_DIR/starfusion.success ]; then
   touch $SETUP_DIR/starfusion.success
 fi
 
-# Install tophat	
-if [ ! -e $SETUP_DIR/tophat.success ]; then	
-  curl -sSL --retry 10 https://ccb.jhu.edu/software/tophat/downloads/tophat-${VER_TOPHAT}.Linux_x86_64.tar.gz > distro.tar.gz	
-  rm -rf distro/*	
-  tar --strip-components 1 -C distro -zxf distro.tar.gz	
-  rm -f distro/AUTHORS distro/LICENSE distro/README	
-  cp -r distro/* $INST_PATH/bin/.	
-  touch $SETUP_DIR/tophat.success	
+# Install tophat
+if [ ! -e $SETUP_DIR/tophat.success ]; then
+  curl -sSL --retry 10 https://ccb.jhu.edu/software/tophat/downloads/tophat-${VER_TOPHAT}.Linux_x86_64.tar.gz > distro.tar.gz
+  rm -rf distro/*
+  tar --strip-components 1 -C distro -zxf distro.tar.gz
+  rm -f distro/AUTHORS distro/LICENSE distro/README
+  cp -r distro/* $INST_PATH/bin/.
+  # patch tophat-fusion-post
+  patch $INST_PATH/bin/tophat-fusion-post $SCRIPT_PATH/patches/tophat-fusion-post.patch
+  chmod +x $INST_PATH/bin/tophat-fusion-post
+  touch $SETUP_DIR/tophat.success
 fi
 
 # Install defuse

diff --git a/build/patches/tophat-fusion-post.patch b/build/patches/tophat-fusion-post.patch
@@ -0,0 +1,74 @@
+--- tophat-fusion-post	2019-10-17 16:06:48.338589724 +0000
++++ tophat-fusion-post.new	2019-10-17 16:08:30.131237030 +0000
+@@ -788,7 +788,7 @@
+
+             same = False
+             for chr_coord in left_chrs:
+-                chr, coord = chr_coord.split(':')
++                chr, coord = chr_coord.rsplit(':', 1)
+                 coord = int(coord)
+                 if chr == chr2 and abs(coord - coord2) < max_intron_len:
+                     same = True
+@@ -798,7 +798,7 @@
+                 continue
+
+             for chr_coord in right_chrs:
+-                chr, coord = chr_coord.split(':')
++                chr, coord = chr_coord.rsplit(':', 1)
+                 coord = int(coord)
+                 if chr == chr1 and abs(coord - coord1) < max_intron_len:
+                     same = True
+@@ -1225,7 +1225,7 @@
+             if line[0] == '@':
+                 if line[1:3] == 'SQ':
+                     line = line[:-1].split('\t')
+-                    contig = line[1].split(':')[1]
++                    contig = line[1].split(':', 1)[1]
+                     if contig not in contigs:
+                         contigs[contig] = len(contigs)
+
+@@ -1533,7 +1533,7 @@
+                     else:
+                         chr1 = value_str
+
+-                    chr1, chr1_coord = chr1.split(':')
++                    chr1, chr1_coord = chr1.rsplit(':', 1)
+                     chr1_left, chr1_right = chr1_coord.split('-')
+                     chr1_left, chr1_right = int(chr1_left), int(chr1_right)
+                     value_dic["chr1"] = chr1
+@@ -1541,7 +1541,7 @@
+                     value_dic["chr1_right"] = chr1_right
+
+                     if chr2:
+-                        chr2, chr2_coord = chr2.split(':')
++                        chr2, chr2_coord = chr2.rsplit(':', 1)
+                         chr2_left, chr2_right = chr2_coord.split('-')
+                         chr2_left, chr2_right = int(chr2_left), int(chr2_right)
+                         value_dic["chr2"] = chr2
+@@ -1592,14 +1592,14 @@
+                     exon_list = curr_transcript[-1]
+
+                     if type == "exon":
+-                        chr, chr_coord = fields[1].split(':')
++                        chr, chr_coord = fields[1].rsplit(':', 1)
+                         chr_left, chr_right = chr_coord.split('-')
+                         chr_left, chr_right = int(chr_left), int(chr_right)
+                         exon_list.append(["exon", chr, chr_left, chr_right])
+                     else:
+                         fusion_left, fusion_right = fields[1].split(' ')
+-                        chr1, chr1_pos = fusion_left.split(':')
+-                        chr2, chr2_pos = fusion_right.split(':')
++                        chr1, chr1_pos = fusion_left.rsplit(':', 1)
++                        chr2, chr2_pos = fusion_right.rsplit(':', 1)
+
+                         chr1_pos, chr2_pos = int(chr1_pos), int(chr2_pos)
+                         exon_list.append(["fusion", chr1, chr1_pos, chr2, chr2_pos])
+@@ -2865,7 +2865,7 @@
+
+
+ def get_version():
+-   return "2.1.0"
++   return "2.1.0-cgpPatched"
+
+
+ def main(argv=None):
diff --git a/cwls/tools/merge_and_mark_dups.cwl b/cwls/tools/merge_and_mark_dups.cwl
@@ -20,7 +20,7 @@ doc: |
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/cgprna:2.4.0"
+    dockerPull: "quay.io/wtsicgp/cgprna:2.4.1"
 
 hints:
   - class: ResourceRequirement

diff --git a/cwls/tools/run-cgprna_bigwig.cwl b/cwls/tools/run-cgprna_bigwig.cwl
@@ -20,7 +20,7 @@ doc: |
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/cgprna:2.4.0"
+    dockerPull: "quay.io/wtsicgp/cgprna:2.4.1"
 
 hints:
   - class: ResourceRequirement

diff --git a/cwls/tools/run-cgprna_htseq-count.cwl b/cwls/tools/run-cgprna_htseq-count.cwl
@@ -20,7 +20,7 @@ doc: |
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/cgprna:2.4.0"
+    dockerPull: "quay.io/wtsicgp/cgprna:2.4.1"
 
 hints:
   - class: ResourceRequirement

diff --git a/cwls/tools/run-cgprna_star-map.cwl b/cwls/tools/run-cgprna_star-map.cwl
@@ -20,7 +20,7 @@ doc: |
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/cgprna:2.4.0"
+    dockerPull: "quay.io/wtsicgp/cgprna:2.4.1"
   - class: InlineJavascriptRequirement
 
 hints:

diff --git a/cwls/tools/run-cgprna_stats.cwl b/cwls/tools/run-cgprna_stats.cwl
@@ -20,7 +20,7 @@ doc: |
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/cgprna:2.4.0"
+    dockerPull: "quay.io/wtsicgp/cgprna:2.4.1"
 
 hints:
   - class: ResourceRequirement

diff --git a/perl/lib/Sanger/CGP/CgpRna.pm b/perl/lib/Sanger/CGP/CgpRna.pm
@@ -36,7 +36,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '2.4.0';
+our $VERSION = '2.4.1';
 our @EXPORT = qw($VERSION);
 
 1;