From bba32e70364d15cddb47c530aa87120422ec965d Mon Sep 17 00:00:00 2001 From: Shriram Bhosle Date: Thu, 11 Aug 2016 11:13:36 +0100 Subject: [PATCH 1/2] added htseq --- .gitignore | 0 CHANGES.md | 2 ++ LICENSE | 0 README.md | 2 +- perl/MANIFEST | 0 perl/Makefile.PL | 0 perl/bin/compare_CN_and_fusion.pl | 0 perl/bin/process_qcstats.pl | 0 perl/docs.tar.gz | Bin perl/lib/Sanger/CGP/CgpRna.pm | 2 +- .../CGP/CompareFusions/FusionAnnotation.pm | 0 .../Sanger/CGP/CompareFusions/Implement.pm | 0 perl/lib/Sanger/CGP/RnaQC/Implement.pm | 0 perl/t/1_pm_compile.t | 0 perl/t/2_pl_compile.t | 0 setup.sh | 28 ++++++++++++++---- 16 files changed, 27 insertions(+), 7 deletions(-) mode change 100644 => 100755 .gitignore create mode 100644 CHANGES.md mode change 100644 => 100755 LICENSE mode change 100644 => 100755 README.md mode change 100644 => 100755 perl/MANIFEST mode change 100644 => 100755 perl/Makefile.PL mode change 100644 => 100755 perl/bin/compare_CN_and_fusion.pl mode change 100644 => 100755 perl/bin/process_qcstats.pl mode change 100644 => 100755 perl/docs.tar.gz mode change 100644 => 100755 perl/lib/Sanger/CGP/CgpRna.pm mode change 100644 => 100755 perl/lib/Sanger/CGP/CompareFusions/FusionAnnotation.pm mode change 100644 => 100755 perl/lib/Sanger/CGP/CompareFusions/Implement.pm mode change 100644 => 100755 perl/lib/Sanger/CGP/RnaQC/Implement.pm mode change 100644 => 100755 perl/t/1_pm_compile.t mode change 100644 => 100755 perl/t/2_pl_compile.t diff --git a/.gitignore b/.gitignore old mode 100644 new mode 100755 diff --git a/CHANGES.md b/CHANGES.md new file mode 100644 index 0000000..f9279c9 --- /dev/null +++ b/CHANGES.md @@ -0,0 +1,2 @@ +### 2.1.0 +* Added HTseq installer for read counting diff --git a/LICENSE b/LICENSE old mode 100644 new mode 100755 diff --git a/README.md b/README.md old mode 100644 new mode 100755 index f786490..97177b9 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ N.B. the path_to_install_to should be the same as the install location used for * [faToTwoBit](http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/) deFuse dependency * [bedtools](https://github.com/arq5x/bedtools2/) Unless already in the install location bin directory * [blastn](http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) Used by tophat-fusion post - +* [HTSeq](https://pypi.python.org/packages/3c/6e/f8dc3500933e036993645c3f854c4351c9028b180c6dcececde944022992/HTSeq-0.6.1p1.tar.gz) used for read counting N.B. samtools is also a dependency but this is installed by PCAP-Core which should have already been installed (see above). If you are planning to use the fusion pipeline, specifically defuse_fusion.pl, the deFuse config.txt file will need to be updated with the installed locations of a number of tools. diff --git a/perl/MANIFEST b/perl/MANIFEST old mode 100644 new mode 100755 diff --git a/perl/Makefile.PL b/perl/Makefile.PL old mode 100644 new mode 100755 diff --git a/perl/bin/compare_CN_and_fusion.pl b/perl/bin/compare_CN_and_fusion.pl old mode 100644 new mode 100755 diff --git a/perl/bin/process_qcstats.pl b/perl/bin/process_qcstats.pl old mode 100644 new mode 100755 diff --git a/perl/docs.tar.gz b/perl/docs.tar.gz old mode 100644 new mode 100755 diff --git a/perl/lib/Sanger/CGP/CgpRna.pm b/perl/lib/Sanger/CGP/CgpRna.pm old mode 100644 new mode 100755 index 51edf06..60efd3e --- 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 = '2.0.18'; +our $VERSION = '2.1.0'; our @EXPORT = qw($VERSION); 1; diff --git a/perl/lib/Sanger/CGP/CompareFusions/FusionAnnotation.pm b/perl/lib/Sanger/CGP/CompareFusions/FusionAnnotation.pm old mode 100644 new mode 100755 diff --git a/perl/lib/Sanger/CGP/CompareFusions/Implement.pm b/perl/lib/Sanger/CGP/CompareFusions/Implement.pm old mode 100644 new mode 100755 diff --git a/perl/lib/Sanger/CGP/RnaQC/Implement.pm b/perl/lib/Sanger/CGP/RnaQC/Implement.pm old mode 100644 new mode 100755 diff --git a/perl/t/1_pm_compile.t b/perl/t/1_pm_compile.t old mode 100644 new mode 100755 diff --git a/perl/t/2_pl_compile.t b/perl/t/2_pl_compile.t old mode 100644 new mode 100755 diff --git a/setup.sh b/setup.sh index b9c7f10..8c05c94 100755 --- a/setup.sh +++ b/setup.sh @@ -46,7 +46,8 @@ SOURCE_GMAP="http://research-pub.gene.com/gmap/src/gmap-gsnap-2015-09-10.tar.gz" SOURCE_BLAT="http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip" SOURCE_FATOTWOBIT="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit" SOURCE_BEDTOOLS="https://github.com/arq5x/bedtools2/releases/download/v2.21.0/bedtools-2.21.0.tar.gz" - +SOURCE_HTSEQ="https://pypi.python.org/packages/3c/6e/f8dc3500933e036993645c3f854c4351c9028b180c6dcececde944022992/HTSeq-0.6.1p1.tar.gz" +VERSION_HTSEQ="0.6.0" done_message () { if [ $? -eq 0 ]; then @@ -154,14 +155,14 @@ fi CHK2=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::Vagrent` if [[ "x$CHK2" == "x" ]] ; then - echo "PREREQUISITE: Please install VAGrENT before proceeding: https://github.com/cancerit/VAGrENT/releases" - exit 1; + echo "PREREQUISITE: Please install VAGrENT before proceeding: https://github.com/cancerit/VAGrENT/releases" + exit 1; fi CHK3=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::Grass` if [[ "x$CHK3" == "x" ]] ; then - echo "PREREQUISITE: Please install Grass before proceeding: https://github.com/cancerit/grass/releases" - exit 1; + echo "PREREQUISITE: Please install Grass before proceeding: https://github.com/cancerit/grass/releases" + exit 1; fi #create a location to build dependencies @@ -424,6 +425,23 @@ else fi done_message "" "Failed to build RSeQC." +# install HTSeq +echo -n "Installing HTSeq ..." +if [ -e $SETUP_DIR/htseq.success ]; then + echo -n " previously installed ..."; +else +( + cd $SETUP_DIR + get_distro "rseqc" $SOURCE_HTSEQ + mkdir -p htseq + tar --strip-components 1 -C htseq -zxf HTSeq-0.6.1p1.tar.gz + cd $SETUP_DIR/htseq && + python ./setup.py install --prefix=$INST_PATH + touch $SETUP_DIR/htseq.success + )>>$INIT_DIR/setup.log 2>&1 +fi +done_message "" "Failed to build HTSeq." + #add bin path for install tests export PATH="$INST_PATH/bin:$PATH" From d65cefdea1b19f3761618013c3ac02b72a4fa836 Mon Sep 17 00:00:00 2001 From: Shriram Bhosle Date: Thu, 11 Aug 2016 11:17:04 +0100 Subject: [PATCH 2/2] updated permissions --- CHANGES.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 CHANGES.md diff --git a/CHANGES.md b/CHANGES.md old mode 100644 new mode 100755