Mercurial > repos > matt-shirley > sra_tools
changeset 27:2295c666e6ce draft
debug prefetch caching and accession input for fastq_dump
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Sat, 29 Jun 2013 15:49:44 -0400 |
| parents | 5f57967aac3e |
| children | 996add6daf36 |
| files | fastq_dump.xml tool_dependencies.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/fastq_dump.xml Sat Jun 29 11:14:03 2013 -0400 +++ b/fastq_dump.xml Sat Jun 29 15:49:44 2013 -0400 @@ -11,8 +11,8 @@ <inputs> <conditional name="input"> <param name="input_select" type="select" label="Select input type"> - <option value="accession">SRR accession</option> - <option value="sra">SRA archive in current history</option> + <option value="accession_number">SRR accession</option> + <option value="file">SRA archive in current history</option> </param> <when value="file"> <param format="sra" name="input" type="data" label="sra archive"/>
--- a/tool_dependencies.xml Sat Jun 29 11:14:03 2013 -0400 +++ b/tool_dependencies.xml Sat Jun 29 15:49:44 2013 -0400 @@ -8,7 +8,7 @@ <action type="shell_command">make static</action> <action type="shell_command">make</action> <action type="make_directory">$INSTALL_DIR/bin</action> - <action type="shell_command">sed -i -e 's/HOME/INSTALL_DIR/g' bin64/ncbi/default.kfg</action> + <action type="shell_command">sed -i -e "s/\$(HOME)/$INSTALL_DIR/g' bin64/ncbi/default.kfg</action> <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> </actions>