---------- Forwarded message ---------- From: מירב . <mer...@gmail.com> Date: Wed, May 29, 2013 at 8:40 PM Subject: Re: [galaxy-dev] installing galaxy To: Ross <ross.laza...@gmail.com>
It worked!! Thank you very mach [?] Merav 2013/5/29 Ross <ross.laza...@gmail.com> > Hi, Merav. > A fully functional Galaxy server relies on a lot of third party software > and the error message you see is probably because you do not have samtools > available - the upload process needs it to make an index for your bam file. > So the solution may be to install the samtools package - eg for ubuntu > something like: > sudo apt-get install samtools > > After that, if you execute > samtools > at a console, you should see something like: > > rlazarus@iaas1-int:~$ samtools > > Program: samtools (Tools for alignments in the SAM format) > Version: 0.1.18 (r982:295) > > Usage: samtools <command> [options] > > Command: view SAM<->BAM conversion > sort sort alignment file > mpileup multi-way pileup > > > > Please take a look at > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies > > > > On Wed, May 29, 2013 at 8:00 PM, מירב . <mer...@gmail.com> wrote: > hello, > > I am installing galaxy locally. > I tried to upload a ".bam" file and I got this message: > > Traceback (most recent call last): > File "/home/user/galaxy_project/tools/data_source/upload.py", line 386, in > <module> > __main__() > File "/home/user/galaxy_project/tools/data_source/upload.py", line 375, in > __main__ > add_file( dataset, registry, json_file, output_path ) > File "/home/user/galaxy_project/tools/data_source/upload.py", line 314, in > add_file > if link_data_only == 'copy_files' and > datatype.dataset_content_needs_grooming( output_path ): > File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 113, > in dataset_content_needs_grooming > version = self._get_samtools_version() > File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 97, > in _get_samtools_version > output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, > stdout=subprocess.PIPE ).communicate()[1] > File "/usr/lib/python2.7/subprocess.py", line 679, in __init__ > errread, errwrite) > File "/usr/lib/python2.7/subprocess.py", line 1259, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory > > > This file uploaded successfully, to the galaxy on the net. > > what can it be? > > thanks for your help > > merav > > > > > > > > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
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___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
