Mercurial > repos > trinity_ctat > align_and_estimate_abundance
changeset 7:78d12a725443 draft
Adding additional requirements for align_and_estimate_abundance.
| author | trinity_ctat |
|---|---|
| date | Tue, 26 Sep 2017 14:31:27 -0400 |
| parents | 12bc09b4a26d |
| children | 28f6d3b8e931 |
| files | align_and_estimate_abundance.xml trinityToolWrapper.py |
| diffstat | 2 files changed, 7 insertions(+), 1 deletions(-) [+] |
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--- a/align_and_estimate_abundance.xml Tue Sep 26 13:58:08 2017 -0400 +++ b/align_and_estimate_abundance.xml Tue Sep 26 14:31:27 2017 -0400 @@ -5,6 +5,10 @@ <requirements> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="2.4.0">trinity</requirement> + <requirement type="package" version="2">bowtie</requirement> + <requirement type="package" >samtools</requirement> + <!-- <requirement type="package" >express</requirement> --> + <requirement type="package" >rsem</requirement> </requirements> <command interpreter="python">
--- a/trinityToolWrapper.py Tue Sep 26 13:58:08 2017 -0400 +++ b/trinityToolWrapper.py Tue Sep 26 14:31:27 2017 -0400 @@ -45,7 +45,9 @@ # Take off the last part of the path (which is the Trinity command) TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) else: - print "Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH." + sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.") + sys.exit() + # get bindir bindir = sys.argv[0]