Mercurial > repos > bebatut > sortmerna
changeset 12:bf5dbe8f7d4c draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 86b25c80bf4746a0bb73002040487242048a40d2-dirty
| author | bebatut |
|---|---|
| date | Tue, 10 Nov 2015 04:05:25 -0500 |
| parents | b8ba70feb088 |
| children | 4016c1db6886 |
| files | sortmerna.xml tool_dependencies.xml |
| diffstat | 2 files changed, 6 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/sortmerna.xml Fri Nov 06 04:40:46 2015 -0500 +++ b/sortmerna.xml Tue Nov 10 04:05:25 2015 -0500 @@ -11,7 +11,7 @@ <version_command> <![CDATA[ -sortmerna --version 2>&1|grep 'SortMeRNA version' +\${SORTMERNADIR}/sortmerna --version 2>&1|grep 'SortMeRNA version' ]]> </version_command> @@ -34,11 +34,11 @@ #end for #end if - indexdb_rna --ref $ref -L $seed_length --max_pos $max_pos + \${SORTMERNADIR}/indexdb_rna --ref $ref -L $seed_length --max_pos $max_pos && - sortmerna + \${SORTMERNADIR}/sortmerna --ref $ref --reads $input_sequence_file --aligned aligned
--- a/tool_dependencies.xml Fri Nov 06 04:40:46 2015 -0500 +++ b/tool_dependencies.xml Tue Nov 10 04:05:25 2015 -0500 @@ -5,8 +5,10 @@ <actions> <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> <action type="autoconf"/> + <action type="change_directory">../</action> + <action type="shell_command">mv sortmerna-2.0/ $INSTALL_DIR/</action> <action type="set_environment"> - <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions>