local install problem with fasta manipulation tools?
Hi I hope I have the correct place to ask for assistance. I've been trying to use a local install of Galaxy. I can upload data and convert formats (FASTq to FASTA) but can't use fasta manipulation tools like width formatter or collapse. I am told "No such file or directory /bin/sh: fasta_formatter: command not found". I don't see these in the list of tools with dependencies. I've used them frequently on the public website so I don't think this is a problem of my file formats. What am i missing? When I try to send a bug report through the local I get an error that mail is not configured. I assume i have not conducted the installation properly but I can't figure out what i have done wrong. I tried to do the local install because my files on the web version have been sitting for many hours waiting to run. Thanks for any help. Beth
I hope I have the correct place to ask for assistance.
Yes, this list is a great place to ask questions about local Galaxy instances.
I've been trying to use a local install of Galaxy. I can upload data and convert formats (FASTq to FASTA) but can't use fasta manipulation tools like width formatter or collapse. I am told "No such file or directory /bin/sh: fasta_formatter: command not found". I don't see these in the list of tools with dependencies. I've used them frequently on the public website so I don't think this is a problem of my file formats. What am i missing? When I try to send a bug report through the local I get an error that mail is not configured.
You need to install analysis tools that you want to use with Galaxy. The tool shed will help with some tools (see Admin --> Tool sheds --> search and browse tool sheds), but others you'll have to install yourself by downloading them and adding them to your PATH.
I tried to do the local install because my files on the web version have been sitting for many hours waiting to run.
There was a problem with our public server's cluster, but it's been fixed and jobs should be running more quickly now. Best, J.
Hi Jeremy, Two things confuse me about this. First, the tools I want to use are not listed under the list of tools with dependencies.. but I still need to install? what is the difference then between tools with dependencies and all the others? Second, in the instructions it suggest that nothing should be listed under the tools when you do a local install... (the instructions I was reading showed screen shots indicating that you configure each tool and it appears in the left hand menu)... when I did the install everything was listed (just not functioning). Is that normal? Thanks Beth On Fri, Jan 18, 2013 at 9:27 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
I hope I have the correct place to ask for assistance.
Yes, this list is a great place to ask questions about local Galaxy instances.
I've been trying to use a local install of Galaxy. I can upload data and convert formats (FASTq to FASTA) but can't use fasta manipulation tools like width formatter or collapse. I am told "No such file or directory /bin/sh: fasta_formatter: command not found". I don't see these in the list of tools with dependencies. I've used them frequently on the public website so I don't think this is a problem of my file formats. What am i missing? When I try to send a bug report through the local I get an error that mail is not configured.
You need to install analysis tools that you want to use with Galaxy. The tool shed will help with some tools (see Admin --> Tool sheds --> search and browse tool sheds), but others you'll have to install yourself by downloading them and adding them to your PATH.
I tried to do the local install because my files on the web version have been sitting for many hours waiting to run.
There was a problem with our public server's cluster, but it's been fixed and jobs should be running more quickly now.
Best, J.
-- -------------------------------- Dr. Elizabeth L. Clare School of Biological and Chemical Sciences Queen Mary, University of London Mile End Road, London E1 4NS Room 1.02, G. E. Fogg Building e.clare@qmul.ac.uk +44 (0)207 882 ext. 5687 School of Biological Sciences University of Bristol, Bristol, UK. Phone: +44 117 954 5909 Website: http://seis.bris.ac.uk/~bzelc/ "If you say yes more often than you say no, you will do interesting things in your life"
Two things confuse me about this. First, the tools I want to use are not listed under the list of tools with dependencies.. but I still need to install? what is the difference then between tools with dependencies and all the others?
If I understand you correctly, here's the answer: tools with dependencies require additional tools in addition to the base tool (e.g. tophat requires bowtie and samtools in addition to the tophat binary). FYI, looking back at your original email, the fasta-formatter that you're missing can be found in the fastx toolkit: http://hannonlab.cshl.edu/fastx_toolkit/index.html The tool dependencies wiki page has been updated to include this information,
Second, in the instructions it suggest that nothing should be listed under the tools when you do a local install... (the instructions I was reading showed screen shots indicating that you configure each tool and it appears in the left hand menu)... when I did the install everything was listed (just not functioning). Is that normal?
The instructions you found are not accurate. Galaxy still comes with a large list of tool wrappers, which are used to populate the list of tools in a local installation. The distinction to make is that the wrapper enables Galaxy to run a tool, but the tool must still be installed before it can be run in Galaxy via the wrapper. In the future, we'll likely have Galaxy versions without any tools previously installed as well as versions that include all the tools on our public server (and perhaps other installations for particular analyses, such as RNA-seq and variation analyses). Good luck, J.
participants (3)
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elclare.evol.biology＠gmail.com -
Elizabeth Clare
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Jeremy Goecks