Mercurial > repos > jjohnson > cdhit
changeset 1:12447208b8cb
Add tool_dependencies
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 06 Sep 2012 21:48:31 -0500 |
| parents | 13900a1ad862 |
| children | c99f307f2bdb |
| files | cd_hit_est.xml tool_dependencies.xml |
| diffstat | 2 files changed, 26 insertions(+), 1 deletions(-) [+] |
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--- a/cd_hit_est.xml Thu Sep 06 22:28:46 2012 -0400 +++ b/cd_hit_est.xml Thu Sep 06 21:48:31 2012 -0500 @@ -1,7 +1,7 @@ <tool id="cd_hit_est" name="CD-HIT-EST" version="1.0"> <description>Cluster a nucleotide dataset into representative sequences</description> <requirements> - <requirement type="package">cd-hit-est</requirement> + <requirement type="package" version="4.6.1">cd-hit-est</requirement> </requirements> <command> cd-hit-est -i $fasta_in -o rep_seq -c $similarity -n $wordsize $strand
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Sep 06 21:48:31 2012 -0500 @@ -0,0 +1,25 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="cd-hit" version="4.6.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz</action> + <action type="shell_command">make openmp=yes</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the cdhit package: + +http://weizhong-lab.ucsd.edu/cd-hit/ + +https://code.google.com/p/cdhit/ + +https://code.google.com/p/cdhit/source/browse/README + + </readme> + </package> +</tool_dependency> +