Hi, I set up a local instance on OS 10.6 and was using some fasta tools but noticed fasta width formatter does not execute. Although it shows in my local web interface I do not see width formatter in the tools.conf.xml, nor does the python script appear in /tools/fasta_tools with the others. I also browsed source from central and dist in fasta_tools and do not see it there either...Thanks for any help. An error occurred running this job:/bin/sh: fasta_formatter: command not found zcat: /Users/Owen/Galaxy/galaxy-dist/database/files/000/dataset_190.dat.Z: No such file or directory
Owen Hardy wrote:
Hi,
I set up a local instance on OS 10.6 and was using some fasta tools but noticed fasta width formatter does not execute. Although it shows in my local web interface I do not see width formatter in the tools.conf.xml, nor does the python script appear in /tools/fasta_tools with the others. I also browsed source from central and dist in fasta_tools and do not see it there either...Thanks for any help.
An error occurred running this job:/bin/sh: fasta_formatter: command not found zcat: /Users/Owen/Galaxy/galaxy-dist/database/files/000/dataset_190.dat.Z: No such file or directory
Hi Owen, Galaxy has various external dependencies for which it provides wrappers - this is one of them, namely, the FASTX-Toolkit, available here: http://hannonlab.cshl.edu/fastx_toolkit/ If you install the Toolkit and insure that it's on your $PATH (i.e. you can run 'fasta_formatter' on the command line), using it in Galaxy should work. --nate
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
I would also recommend getting the latest XML wrappers from here: http://hannonlab.cshl.edu/fastx_toolkit/download.html Or at least changing "zcat" to "cat" in your XML files, as "zcat" on Mac-OS behaves differently than linux's (and that is the source of your error message). Nate Coraor wrote, On 05/11/2011 10:22 AM:
Owen Hardy wrote:
Hi,
I set up a local instance on OS 10.6 and was using some fasta tools but noticed fasta width formatter does not execute. Although it shows in my local web interface I do not see width formatter in the tools.conf.xml, nor does the python script appear in /tools/fasta_tools with the others. I also browsed source from central and dist in fasta_tools and do not see it there either...Thanks for any help.
An error occurred running this job:/bin/sh: fasta_formatter: command not found zcat: /Users/Owen/Galaxy/galaxy-dist/database/files/000/dataset_190.dat.Z: No such file or directory
Hi Owen,
Galaxy has various external dependencies for which it provides wrappers - this is one of them, namely, the FASTX-Toolkit, available here:
http://hannonlab.cshl.edu/fastx_toolkit/
If you install the Toolkit and insure that it's on your $PATH (i.e. you can run 'fasta_formatter' on the command line), using it in Galaxy should work.
--nate
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Assaf Gordon -
Nate Coraor -
Owen Hardy