Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 66:ef13be78c5fc draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Tue, 20 May 2014 09:06:50 -0400 |
| parents | 19360b35f760 |
| children | 6099ef001118 |
| files | samtools-parallel-mpileup.xml tool_dependencies.xml varscan_mpileup2snp_from_bam.xml |
| diffstat | 3 files changed, 23 insertions(+), 98 deletions(-) [+] |
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--- a/samtools-parallel-mpileup.xml Wed Mar 05 11:08:26 2014 -0500 +++ b/samtools-parallel-mpileup.xml Tue May 20 09:06:50 2014 -0400 @@ -3,7 +3,8 @@ <description>Samtools mpileup (supporting parallelization)</description> <requirements> <requirement type="package" version="0.1.19">samtools-parallel-mpileup</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> + <!-- <requirement type="package" version="0.1.19">samtools</requirement> --> + <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement> </requirements> <command> #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
--- a/tool_dependencies.xml Wed Mar 05 11:08:26 2014 -0500 +++ b/tool_dependencies.xml Tue May 20 09:06:50 2014 -0400 @@ -1,10 +1,23 @@ <?xml version="1.0"?> <tool_dependency> + + <package name="ncurses" version="5.9"> + <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <!-- Optimized samtools (for threaded mpileup) --> <package name="samtools-parallel-mpileup" version="0.1.19"> <install version="1.0"> <actions> - <action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup && cd samtools-parallel-mpileup && cd $(ls |grep samtools-) && make && cp samtools ../samtools-parallel-mpileup</action> + <action type="set_environment_for_install"> + <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="ncurses" version="5.9" /> + </repository> + </action> + <action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup && cd samtools-parallel-mpileup</action> + <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action> + <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> + <action type="shell_command">cd samtools-parallel-mpileup && cd $(ls |grep samtools-) && make && cp samtools ../samtools-parallel-mpileup</action> <action type="move_file"> <source>samtools-parallel-mpileup</source> <destination>$INSTALL_DIR/bin</destination> @@ -20,101 +33,11 @@ </readme> </package> - <!-- Classical samtools (doesn't support threaded mpileup) --> - <package name="samtools" version="0.1.19"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> - <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> - <action type="shell_command">make</action> - <action type="shell_command">chmod ugo+rx misc/*.p?</action> - <action type="shell_command">mkdir misc/bin</action> - <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bcftools/bcftools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bcftools/vcfutils.pl</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_directory_files"> - <source_directory>misc/bin</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Program: samtools (Tools for alignments in the SAM format) -Version: 0.1.19 - -Usage: samtools <command> [options] - -Command: view SAM<->BAM conversion - sort sort alignment file - mpileup multi-way pileup - depth compute the depth - faidx index/extract FASTA - tview text alignment viewer - index index alignment - idxstats BAM index stats (r595 or later) - fixmate fix mate information - flagstat simple stats - calmd recalculate MD/NM tags and '=' bases - merge merge sorted alignments - rmdup remove PCR duplicates - reheader replace BAM header - cat concatenate BAMs - targetcut cut fosmid regions (for fosmid pool only) - phase phase heterozygotes - -This also installs bcftools and misc utility commands: - bcftools - vcfutils.pl - ace2sam - bamcheck - blast2sam.pl - bowtie2sam.pl - export2sam.pl - interpolate_sam.pl - maq2sam-long - maq2sam-short - md5fa - md5sum-lite - novo2sam.pl - psl2sam.pl - sam2vcf.pl - samtools.pl - soap2sam.pl - varfilter.py - wgsim - wgsim_eval.pl - zoom2sam.pl - </readme> - </package> + <package name="package_samtools_0_1_19" version="0.1.19"> + <repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> - <package name="VarScan" version="2.3.6"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action> - <action type="move_file"> - <source>VarScan.v2.3.6.jar</source> - <destination>$INSTALL_DIR/jars</destination> - </action> - <action type="set_environment"> - <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable> - </action> - </actions> - </install> - <readme> - Downloads VarScan2. - </readme> + <package name="varscan" version="2.3.6"> + <repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency> \ No newline at end of file
--- a/varscan_mpileup2snp_from_bam.xml Wed Mar 05 11:08:26 2014 -0500 +++ b/varscan_mpileup2snp_from_bam.xml Tue May 20 09:06:50 2014 -0400 @@ -4,7 +4,8 @@ <requirements> <requirement type="package" version="0.1.19">samtools-parallel-mpileup</requirement> <requirement type="package" version="2.3.6">VarScan</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> + <!-- <requirement type="package" version="0.1.19">samtools</requirement> --> + <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement> </requirements> <command> #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1