Mercurial > repos > bgruening > bismark
changeset 22:047eb877b6f0 draft
Uploaded
author | iuc |
---|---|
date | Sun, 28 Jun 2015 07:23:35 -0400 |
parents | 507901240749 |
children | 4084128e7cca |
files | bismark_bowtie2_wrapper.xml bismark_bowtie_wrapper.xml bismark_methylation_extractor.xml tool_dependencies.xml |
diffstat | 4 files changed, 15 insertions(+), 67 deletions(-) [+] |
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--- a/bismark_bowtie2_wrapper.xml Wed Feb 11 16:21:27 2015 -0500 +++ b/bismark_bowtie2_wrapper.xml Sun Jun 28 07:23:35 2015 -0400 @@ -1,11 +1,10 @@ -<tool id="bismark_bowtie2" name="Bismark" version="0.10.2"> +<tool id="bismark_bowtie2" name="Bismark" version="0.14.3"> <!-- Wrapper compatible with Bismark version 0.10 --> <description>bisulfite mapper (bowtie2)</description> <!--<version_command>bismark version</version_command>--> <requirements> - <requirement type="set_environment">SCRIPT_PATH</requirement> <requirement type="package" version="0.1.19">samtools</requirement> - <requirement type="package" version="2.1.0">bowtie2</requirement> + <requirement type="package" version="2.2.5">bowtie2</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -20,7 +19,7 @@ ## Change this to accommodate the number of threads you have available. --num-threads "\${GALAXY_SLOTS:-24}" - --bismark_path \$SCRIPT_PATH + --bismark_path $__tool_directory__ --bowtie2
--- a/bismark_bowtie_wrapper.xml Wed Feb 11 16:21:27 2015 -0500 +++ b/bismark_bowtie_wrapper.xml Sun Jun 28 07:23:35 2015 -0400 @@ -1,11 +1,10 @@ -<tool id="bismark_bowtie" name="Bismark" version="0.10.2"> +<tool id="bismark_bowtie" name="Bismark" version="0.14.3"> <!-- Wrapper compatible with Bismark version 0.10 --> <description>bisulfite mapper (bowtie)</description> <!--<version_command>bismark version</version_command>--> <requirements> - <requirement type="set_environment">SCRIPT_PATH</requirement> <requirement type="package" version="0.1.19">samtools</requirement> - <requirement type="package" version="0.12.8">bowtie</requirement> + <requirement type="package" version="1.0.0">bowtie</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -17,7 +16,7 @@ <![CDATA[ bismark_wrapper.py - --bismark_path \$SCRIPT_PATH + --bismark_path $__tool_directory__ ## ## Bismark Genome Preparation, if desired.
--- a/bismark_methylation_extractor.xml Wed Feb 11 16:21:27 2015 -0500 +++ b/bismark_methylation_extractor.xml Sun Jun 28 07:23:35 2015 -0400 @@ -1,11 +1,10 @@ -<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.10.2"> +<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.14.3"> <!-- Wrapper compatible with Bismark version 0.10 --> <description>Reports on methylation status of reads mapped by Bismark</description> <!--<version_command>bismark_methylation_extractor version</version_command>--> <requirements> - <requirement type="set_environment">SCRIPT_PATH</requirement> - <requirement type="package" version="0.12.8">bowtie</requirement> - <requirement type="package" version="2.1.0">bowtie2</requirement> + <requirement type="package" version="1.0.0">bowtie</requirement> + <requirement type="package" version="2.2.5">bowtie2</requirement> </requirements> <parallelism method="basic"></parallelism> <command interpreter="python"> @@ -14,7 +13,7 @@ --infile $input - --bismark_path \$SCRIPT_PATH + --bismark_path $__tool_directory__ #if $singlePaired.sPaired == "single": --single-end
--- a/tool_dependencies.xml Wed Feb 11 16:21:27 2015 -0500 +++ b/tool_dependencies.xml Sun Jun 28 07:23:35 2015 -0400 @@ -1,61 +1,12 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <set_environment version="1.0"> - <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - <package name="bowtie2" version="2.1.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bowtie2</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bowtie2-align</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bowtie2-build</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Compiling bowtie2 requires zlib and libpthread to be present on your system. - </readme> + <package name="bowtie2" version="2.2.5"> + <repository changeset_revision="e627be2bba58" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="bowtie" version="0.12.8"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bowtie</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bowtie-inspect</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bowtie-build</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> - </readme> + <package name="bowtie" version="1.0.0"> + <repository changeset_revision="0931da782b5d" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>