Mercurial > repos > nick > duplex
changeset 6:e9f9b1d1c6fb draft
planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
| author | nick |
|---|---|
| date | Mon, 23 Nov 2015 19:01:06 -0500 |
| parents | 9d46c9ca7ceb |
| children | bf7478987a6d |
| files | make_families.xml tool_dependencies.xml |
| diffstat | 2 files changed, 5 insertions(+), 13 deletions(-) [+] |
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--- a/make_families.xml Mon Nov 23 18:46:22 2015 -0500 +++ b/make_families.xml Mon Nov 23 19:01:06 2015 -0500 @@ -3,9 +3,9 @@ <description>from duplex sequencing data</description> <requirements> <requirement type="package" version="0.1">duplex</requirement> - <!-- <requirement type="set_environment">DUPLEX_DIR</requirement> --> + <requirement type="set_environment">DUPLEX_DIR</requirement> </requirements> - <command>paste $fastq1 $fastq2 + <command>echo "\$DUPLEX_DIR" >&2 && paste $fastq1 $fastq2 | paste - - - - | awk -f \$DUPLEX_DIR/make-barcodes.awk -v TAG_LEN=$taglen -v INVARIANT=$invariant | sort
--- a/tool_dependencies.xml Mon Nov 23 18:46:22 2015 -0500 +++ b/tool_dependencies.xml Mon Nov 23 19:01:06 2015 -0500 @@ -8,17 +8,9 @@ <actions> <action type="download_by_url">https://github.com/makrutenko/duplex/archive/master.tar.gz</action> <action type="shell_command">make</action> - <action type="move_file"> - <source>*.so</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>*.py</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>*.awk</source> - <destination>$INSTALL_DIR</destination> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> </action> <action type="set_environment"> <environment_variable action="set_to" name="DUPLEX_DIR">$INSTALL_DIR</environment_variable>