Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 86:c1424388f08b draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
author | yhoogstrate |
---|---|
date | Thu, 05 Nov 2015 03:45:02 -0500 |
parents | ddbaf017720a |
children | f7798cd80cf5 |
files | samtools-parallel-mpileup.xml tool_dependencies.xml varscan_mpileup2snp.xml varscan_mpileup2snp_from_bam.xml |
diffstat | 4 files changed, 66 insertions(+), 54 deletions(-) [+] |
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--- a/samtools-parallel-mpileup.xml Wed Nov 19 10:02:46 2014 -0500 +++ b/samtools-parallel-mpileup.xml Thu Nov 05 03:45:02 2015 -0500 @@ -2,7 +2,7 @@ <tool id="samtools_parallel_mpileup" name="Samtools parallel mpileup" version="0.1.19a.a"> <description>Samtools mpileup (supporting parallelization)</description> <requirements> - <requirement type="package" version="5.9">ncurses</requirement> + <requirement type="package" version="6.0">ncurses</requirement> <requirement type="package" version="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement> <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement> </requirements> @@ -268,4 +268,12 @@ http://testtoolshed.g2.bx.psu.edu/ </help> + <citation type="bibtex"> + @unpublished{samtools_parallel_mpileup, + author = {Youri Hoogstrate}, + title = { Samtools parallel-mpileup, fork of classical samtools }, + year = 2014, + url = { https://github.com/yhoogstrate/parallel-mpileup } + } + </citation> </tool> \ No newline at end of file
--- a/tool_dependencies.xml Wed Nov 19 10:02:46 2014 -0500 +++ b/tool_dependencies.xml Thu Nov 05 03:45:02 2015 -0500 @@ -1,55 +1,50 @@ <?xml version="1.0"?> <tool_dependency> - <!-- - <package name="ncurses" version="5.9"> - <repository name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" /> - </package> - --> - - <package name="ncurses" version="5.9"> - <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - - <package name="samtools" version="0.1.19"> - <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - - <package name="samtools_parallel_mpileup_0_1_19a" version="0.1.19a"> - <install version="1.0"> - <actions> - <action type="set_environment_for_install"> - <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" toolshed="https://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 ; - cd $(ls |grep samtools-) ; - - sed -i 's/-lcurses/-lncurses/' Makefile ; - sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ; - - make ; - cp samtools ../samtools-parallel-mpileup</action> - <action type="move_file"> - <source>samtools-parallel-mpileup/samtools-parallel-mpileup</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - Downloads and installs a modified version of samtools, able to paralellize the mpileup function. - </readme> - </package> - - <package name="varscan" version="2.3.6"> - <repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> + <package name="ncurses" version="6.0"> + <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + + <package name="samtools" version="0.1.19"> + <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + + <package name="samtools_parallel_mpileup_0_1_19a" version="0.1.19a"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://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 ; + cd $(ls |grep samtools-) ; + + sed -i 's/-lcurses/-lncurses/' Makefile ; + sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ; + + make ; + cp samtools ../samtools-parallel-mpileup + </action> + <action type="move_file"> + <source>samtools-parallel-mpileup/samtools-parallel-mpileup</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + Downloads and installs a modified version of samtools, able to paralellize the mpileup function. + </readme> + </package> + + <package name="varscan" version="2.3.6"> + <repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> </tool_dependency>
--- a/varscan_mpileup2snp.xml Wed Nov 19 10:02:46 2014 -0500 +++ b/varscan_mpileup2snp.xml Thu Nov 05 03:45:02 2015 -0500 @@ -4,6 +4,9 @@ <requirements> <requirement type="package" version="2.3.6">varscan</requirement> </requirements> + + <version_command>java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1</version_command> + <command> cat $mpileup_input | java -Xmx64G @@ -26,7 +29,7 @@ #end if 2> stderr.txt - > $snv_output ; + > $snv_output ; cat stderr.txt </command> @@ -123,4 +126,7 @@ http://testtoolshed.g2.bx.psu.edu/ </help> + <citations> + <citation type="doi">10.1101/gr.129684.111</citation> + </citations> </tool> \ No newline at end of file
--- a/varscan_mpileup2snp_from_bam.xml Wed Nov 19 10:02:46 2014 -0500 +++ b/varscan_mpileup2snp_from_bam.xml Thu Nov 05 03:45:02 2015 -0500 @@ -323,4 +323,7 @@ http://testtoolshed.g2.bx.psu.edu/ </help> + <citations> + <citation type="doi">10.1101/gr.129684.111</citation> + </citations> </tool> \ No newline at end of file