Mercurial > repos > trinity_ctat > align_and_estimate_abundance
changeset 8:28f6d3b8e931 draft
Adjusting requirements.
| author | trinity_ctat |
|---|---|
| date | Tue, 26 Sep 2017 14:54:33 -0400 |
| parents | 78d12a725443 |
| children | b6152cc26ffd |
| files | align_and_estimate_abundance.xml trinityToolWrapper.py |
| diffstat | 2 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/align_and_estimate_abundance.xml Tue Sep 26 14:31:27 2017 -0400 +++ b/align_and_estimate_abundance.xml Tue Sep 26 14:54:33 2017 -0400 @@ -5,10 +5,9 @@ <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> + <requirement type="package">bowtie2</requirement> + <requirement type="package">samtools</requirement> + <requirement type="package">rsem</requirement> </requirements> <command interpreter="python">
--- a/trinityToolWrapper.py Tue Sep 26 14:31:27 2017 -0400 +++ b/trinityToolWrapper.py Tue Sep 26 14:54:33 2017 -0400 @@ -24,8 +24,9 @@ try: pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE) except: + msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.".format(sys.argv[0]) + sys.stderr.write(msg) t, v, tb = sys.exc_info() - sys.stderr.write("You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.".format(sys.argv[0])) raise t, v, tb else: TrinityPath, err_info = pipe1.communicate()