Mercurial > repos > kevyin > meme_chip
changeset 16:c3e0e0a0ae09 draft
Uploaded
author | kevyin |
---|---|
date | Mon, 12 Nov 2012 19:34:55 -0500 |
parents | a6a92a8fe166 |
children | 5bb9eb050e57 |
files | README meme_chip_wrapper.xml tool_dependencies.xml |
diffstat | 3 files changed, 19 insertions(+), 11 deletions(-) [+] |
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--- a/README Mon Nov 12 01:17:03 2012 -0500 +++ b/README Mon Nov 12 19:34:55 2012 -0500 @@ -1,11 +1,19 @@ Meme-chip wrapper for Galaxy +=========================================: ========Installation instructions========: -First make sure meme is installed and accessible from the command line. +=========================================: +The tool_dependencies.xml can attempt to install meme in a folder specific for this tool. +(such as bwa_wrappers) + +The procedure does NOT download motif databases you will need to download them yourself + Meme-chip assumes the meme tools are in PATH. +Make sure meme is accessible + ========Tool data table conf======== -Check the entry is in tool_data_table_conf.xml +Check the meme_chip_motifs entry is in tool_data_table_conf.xml ========Tool loc file======== @@ -22,9 +30,11 @@ After running delete the loc entries with multiple paths eg. All Vertebrates +=========================================: LICENSE for this wrapper: +=========================================: Kevin Ying -Garvan Institute http://www.garvan.org.au -GVL https://genome.edu.au/wiki/GVL +Garvan Institute: http://www.garvan.org.au +GVL: https://genome.edu.au/wiki/GVL http://opensource.org/licenses/mit-license.php
--- a/meme_chip_wrapper.xml Mon Nov 12 01:17:03 2012 -0500 +++ b/meme_chip_wrapper.xml Mon Nov 12 19:34:55 2012 -0500 @@ -1,4 +1,4 @@ -<tool id="meme_chip_wrapper" name="meme-chip" version="1.2.1"> +<tool id="meme_chip_wrapper" name="meme-chip" version="1.2.3"> <requirements> <requirement type="package" version="4.9.0">meme</requirement> </requirements>
--- a/tool_dependencies.xml Mon Nov 12 01:17:03 2012 -0500 +++ b/tool_dependencies.xml Mon Nov 12 19:34:55 2012 -0500 @@ -3,12 +3,10 @@ <package name="meme" version="4.9.0"> <install version="1.0"> <actions> - <!--<action type="download_by_url">ftp://ftp.ebi.edu.au/pub/software/MEME/r4.9.0/rc5/meme_4.9.0.tar.gz</action>--> - <action type="shell_command">touch dummyfile</action> - <action type="move_file"> - <source>dummyfile</source> - <destination>$INSTALL_DIR/bin</destination> - </action> + <action type="download_by_url">ftp://ftp.ebi.edu.au/pub/software/MEME/r4.9.0/rc5/meme_4.9.0.tar.gz</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> + <action type="shell_command">make</action> + <action type="shell_command">make install</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action>