Trinity RnaSeq Protocol

Question

[mazdarsophia]

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.

[mazdarsophia]

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

[WouterDeCoster]

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.

[mazdarsophia]

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

Answer 1

[Medhat]

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