Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 68:bc398d6bac85 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Tue, 20 May 2014 09:19:36 -0400 |
| parents | 6099ef001118 |
| children | 74c06a2e4a69 |
| files | samtools-parallel-mpileup.xml tool_dependencies.xml tool_dependencies_plain.xml varscan_mpileup2snp.xml varscan_mpileup2snp_from_bam.xml |
| diffstat | 5 files changed, 5 insertions(+), 168 deletions(-) [+] |
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--- a/samtools-parallel-mpileup.xml Tue May 20 09:12:25 2014 -0400 +++ b/samtools-parallel-mpileup.xml Tue May 20 09:19:36 2014 -0400 @@ -2,8 +2,7 @@ <tool id="samtools_parallel_mpileup" name="Samtools parallel mpileup"> <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_parallel_mpileup</requirement> <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement> </requirements> <command>
--- a/tool_dependencies.xml Tue May 20 09:12:25 2014 -0400 +++ b/tool_dependencies.xml Tue May 20 09:19:36 2014 -0400 @@ -6,7 +6,7 @@ </package> <!-- Optimized samtools (for threaded mpileup) --> - <package name="samtools-parallel-mpileup" version="0.1.19"> + <package name="samtools_parallel_mpileup" version="0.1.19"> <install version="1.0"> <actions> <action type="set_environment_for_install">
--- a/tool_dependencies_plain.xml Tue May 20 09:12:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,161 +0,0 @@ - - <!-- 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">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Program: samtools (Tools for alignments in the SAM format) -Version: 0.1.19 - -Usage: samtools <command> [options] - -Command: view SAM<->BAM conversion - sort sort alignment file - mpileup multi-way pileup - depth compute the depth - faidx index/extract FASTA - tview text alignment viewer - index index alignment - idxstats BAM index stats (r595 or later) - fixmate fix mate information - flagstat simple stats - calmd recalculate MD/NM tags and '=' bases - merge merge sorted alignments - rmdup remove PCR duplicates - reheader replace BAM header - cat concatenate BAMs - targetcut cut fosmid regions (for fosmid pool only) - phase phase heterozygotes - -This also installs bcftools and misc utility commands: - bcftools - vcfutils.pl - ace2sam - bamcheck - blast2sam.pl - bowtie2sam.pl - export2sam.pl - interpolate_sam.pl - maq2sam-long - maq2sam-short - md5fa - md5sum-lite - novo2sam.pl - psl2sam.pl - sam2vcf.pl - samtools.pl - soap2sam.pl - varfilter.py - wgsim - wgsim_eval.pl - zoom2sam.pl - </readme> - </package> - --> - - - - - <!-- - <package name="VarScan" version="2.3.6"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action> - <action type="move_file"> - <source>VarScan.v2.3.6.jar</source> - <destination>$INSTALL_DIR/jars</destination> - </action> - <action type="set_environment"> - <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable> - </action> - </actions> - </install> - <readme> - Downloads VarScan2. - </readme> - </package> -</tool_dependency> ---> - - -<!-- -< ? xml version="1.0" ? > -<tool_dependency> - <package name="ncurses" version="5.9"> - <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="0.1.19"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> - <action type="set_environment_for_install"> - <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="ncurses" version="5.9" /> - </repository> - </action> - <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action> - <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$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 - -Requirements: libncurses header files - </readme> - </package> \ No newline at end of file
--- a/varscan_mpileup2snp.xml Tue May 20 09:12:25 2014 -0400 +++ b/varscan_mpileup2snp.xml Tue May 20 09:19:36 2014 -0400 @@ -2,7 +2,7 @@ <tool id="varscan_mpileup2snp" name="VarScan2 Call SNPs from a mpileup file"> <description>VarScan2 SNP/SNV detection; directly from a *.mpileup file.</description> <requirements> - <requirement type="package" version="2.3.6">VarScan</requirement> + <requirement type="package" version="2.3.6">varscan</requirement> </requirements> <command> cat $mpileup_input | java
--- a/varscan_mpileup2snp_from_bam.xml Tue May 20 09:12:25 2014 -0400 +++ b/varscan_mpileup2snp_from_bam.xml Tue May 20 09:19:36 2014 -0400 @@ -2,9 +2,8 @@ <tool id="varscan_mpileup2snp_from_bam" name="VarScan2 Call SNPs from BAM"> <description>VarScan2 SNP/SNV detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unncessairy I/O overhead and increase performance.</description> <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_parallel_mpileup</requirement> + <requirement type="package" version="2.3.6">varscan</requirement> <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement> </requirements> <command>