Mercurial > repos > fubar > fastqc
changeset 2:40b80f54e1a7 draft
Uploaded
author | fubar |
---|---|
date | Tue, 04 Jun 2013 22:18:27 -0400 |
parents | 95064b2e024f |
children | 7e6db50c9d47 |
files | FastQC/rgFastQC.xml FastQC/tool_dependencies.xml |
diffstat | 2 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/FastQC/rgFastQC.xml Tue Jun 04 21:36:30 2013 -0400 +++ b/FastQC/rgFastQC.xml Tue Jun 04 22:18:27 2013 -0400 @@ -1,13 +1,14 @@ <tool name="FastQC: Comprehensive QC" id="fastqc" version="0.53"> <description>reporting for short read sequence</description> <command interpreter="python"> - rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_BINARY_PATH" + rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" #if $contaminants.dataset and str($contaminants) > '' -c "$contaminants" #end if +-e fastqc </command> <requirements> - <requirement type="set_environment">FASTQC_BINARY_PATH</requirement> + <requirement type="set_environment">FASTQC_INSTALL_PATH</requirement> <requirement type="package" version="0.10.1">FastQC</requirement> </requirements> <inputs>
--- a/FastQC/tool_dependencies.xml Tue Jun 04 21:36:30 2013 -0400 +++ b/FastQC/tool_dependencies.xml Tue Jun 04 22:18:27 2013 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <set_environment version="1.0"> - <environment_variable name="FASTQC_BINARY_PATH" action="set_to">$INSTALL_DIR/FastQC/fastqc</environment_variable> + <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/FastQC/fastqc</environment_variable> </set_environment> <package name="FastQC" version="0.10.1"> <install version="1.0"> @@ -12,6 +12,9 @@ <destination_directory>$INSTALL_DIR/FastQC</destination_directory> </action> <action type="shell_command">chmod ugo+x $INSTALL_DIR/FastQC/fastqc</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/FastQC</environment_variable> + </action> </actions> </install> <readme>You need a working unzip command line executable to install this tool and a suitable working Java run time environment