Question: Trinity RnaSeq Protocol
0
gravatar for mazdarsophia
15 months ago by
mazdarsophia0 wrote:

I'm trying to run Trinityrnaseq-protocol , the latest version , but it doesn't work . It display to me this error : "You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this" How can I fix this issues ? Thnx in advance.

assembly • 438 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by mazdarsophia0

How can I do that if I'm runing the tool on Galaxy ?

ADD REPLYlink written 15 months ago by mazdarsophia0

Hi mazdarsophia, you commented on your own post, not on the post of Medhat. It would have been good too to mention from the beginning that you are using Galaxy.

ADD REPLYlink written 15 months ago by WouterDeCoster24k

Could you help me in order to find a solution and let the tool work in galaxy ? thnx in advance

ADD REPLYlink written 15 months ago by mazdarsophia0
0
gravatar for Medhat
15 months ago by
Medhat7.2k
Poland
Medhat7.2k wrote:

Assuming you are using some kind of linux you need to use export

export TRINITY_BASE_DIR=/location/of/installation/directory

is it is searching for it in the cood here

if os.environ.has_key('TRINITY_BASE_DIR'):
    TRINITY_BASE_DIR = os.environ['TRINITY_BASE_DIR'];
else:
    sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
sys.exit()

after exporting it you can see all the exported variable using this command

export -p
ADD COMMENTlink modified 15 months ago • written 15 months ago by Medhat7.2k
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