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DaehwanKimLab / tophat

Spliced read mapper for RNA-Seq
http://ccb.jhu.edu/software/tophat
Boost Software License 1.0
91 stars 46 forks source link

Small portability fix and a typo. #15

Closed cbrueffer closed 8 years ago

cbrueffer commented 9 years ago

Even better would be just using #!/bin/sh, since I don't think any bash-specific features are being used here.

gpertea commented 8 years ago

Thank you, typo fixed. About replacing /bin/bash ... I don't know, seems a bit silly to call a basic shell interpreter through env just because of one relatively rare OS exception -- sorry for the apparent lack of FreeBSD love but pretty much every other platform has /bin/bash (even that fancy FreeBSD window dresser called OS X).

cbrueffer commented 8 years ago

True; on the other hand, the change is inconsequential on Linux, but makes the software work out of the box on several other OS :-)

Do any of the scripts even use bash specific features? If not, using #!/bin/sh would be an even better option that's guaranteed to work on any Unix.

gpertea commented 8 years ago

OK, as I had to mess up with the tophat2 script again anyway, I'll just follow your suggestion of using env to find bash, it is indeed more portable this way.