Re: [galaxy-dev] Unable to upload bam files as links to my local galaxy instance - please help!

2016-12-05 Thread Peter Cock 
Galaxy itself needs samtools, and this is not handled via the
Tool Shed which only does dependencies of Galaxy Tools.

I don't think the website is clear enough about this,
https://wiki.galaxyproject.org/Admin/GetGalaxy
just points at
https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

Which version of Galaxy are you using? Older versions had
to have an older samtools (which had a different API for
using samtools sort).

Peter

On Mon, Dec 5, 2016 at 12:36 PM, Konstantinos Voutetakis  wrote:
> Dear Sir(s),
>
> I have consumed a few days in order to resolve this issue but nothing! I
> have installed all the SAM tools of public Galaxy in my local galaxy via the
> Toolshed (installing automatically all the dependencies were needed). I have
> also export the path of the executable file SAMtools from bin folder to my
> Galaxy path and I take the following error during uploading:
>
> Traceback (most recent call last):
>   File "/home/user/galaxy/tools/data_source/upload.py", line 434, in
> 
> __main__()
>   File "/home/user/galaxy/tools/data_source/upload.py", line 423, in
> __main__
> add_file( dataset, registry, json_file, output_path )
>   File "/home/user/galaxy/tools/data_source/upload.py", line 317, in
> add_file
> if datatype.dataset_content_needs_grooming( dataset.path ):
>   File "/home/user/galaxy/lib/galaxy/datatypes/binary.py", line 251, in
> dataset_content_needs_grooming
> version = self._get_samtools_version()
>   File "/home/user/galaxy/lib/galaxy/datatypes/binary.py", line 212, in
> _get_samtools_version
> raise Exception(message)
> Exception: Attempting to use functionality requiring samtools, but it cannot
> be located on Galaxy's PATH.
>
> When I am in my galaxy folder (from where I connect to my galaxy server) and
> I type samtools in the terminal I take:
> Program: samtools (Tools for alignments in the SAM format)
> Version: 0.1.19-44428cd
>
> Usage:   samtools  [options]
>
> Command: viewSAM<->BAM conversion
>  sortsort alignment file
>  mpileup multi-way pileup
>  depth   compute the depth
>  faidx   index/extract FASTA
>  tview   text alignment viewer
>  index   index alignment
>  idxstatsBAM index stats (r595 or later)
>  fixmate fix mate information
>  flagstatsimple stats
>  calmd   recalculate MD/NM tags and '=' bases
>  merge   merge sorted alignments
>  rmdup   remove PCR duplicates
>  reheaderreplace BAM header
>  cat concatenate BAMs
>  bedcov  read depth per BED region
>  targetcut   cut fosmid regions (for fosmid pool only)
>  phase   phase heterozygotes
>  bamshuf shuffle and group alignments by name
>
> What can I do? I installed galaxy to my pc (ubuntu 16.04) before two weeks
> and it is up to date. I would be grateful for your help.
>
> Yours sincerely,
> Kostas
>
> --
> Konstantinos G. Voutetakis, MSc - Research Officer
> National Hellenic Research Foundation (N.H.R.F.)
> Institute of Biology, Medicinal Chemistry and Biotechnology
> 48 Vas. Constantinou Ave., Athens 11635
> Greece
> --
> 
> tel.: +30-210-7273894
> e-mail: kvou...@eie.gr
>
> ___
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[galaxy-dev] Unable to upload bam files as links to my local galaxy instance - please help!

2016-12-05 Thread Konstantinos Voutetakis 
Dear Sir(s),

I have consumed a few days in order to resolve this issue but nothing! I
have installed all the SAM tools of public Galaxy in my local galaxy via
the Toolshed (installing automatically all the dependencies were needed). I
have also export the path of the executable file SAMtools from bin folder
to my Galaxy path and I take the following error during uploading:

Traceback (most recent call last):
  File "/home/user/galaxy/tools/data_source/upload.py", line 434, in 
__main__()
  File "/home/user/galaxy/tools/data_source/upload.py", line 423, in __main__
add_file( dataset, registry, json_file, output_path )
  File "/home/user/galaxy/tools/data_source/upload.py", line 317, in add_file
if datatype.dataset_content_needs_grooming( dataset.path ):
  File "/home/user/galaxy/lib/galaxy/datatypes/binary.py", line 251,
in dataset_content_needs_grooming
version = self._get_samtools_version()
  File "/home/user/galaxy/lib/galaxy/datatypes/binary.py", line 212,
in _get_samtools_version
raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it
cannot be located on Galaxy's PATH.

When I am in my galaxy folder (from where I connect to my galaxy server)
and I type samtools in the terminal I take:
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd

Usage:   samtools  [options]

Command: viewSAM<->BAM conversion
 sortsort alignment file
 mpileup multi-way pileup
 depth   compute the depth
 faidx   index/extract FASTA
 tview   text alignment viewer
 index   index alignment
 idxstatsBAM index stats (r595 or later)
 fixmate fix mate information
 flagstatsimple stats
 calmd   recalculate MD/NM tags and '=' bases
 merge   merge sorted alignments
 rmdup   remove PCR duplicates
 reheaderreplace BAM header
 cat concatenate BAMs
 bedcov  read depth per BED region
 targetcut   cut fosmid regions (for fosmid pool only)
 phase   phase heterozygotes
 bamshuf shuffle and group alignments by name

What can I do? I installed galaxy to my pc (ubuntu 16.04) before two weeks
and it is up to date. I would be grateful for your help.

Yours sincerely,
Kostas

-- 
Konstantinos G. Voutetakis, MSc - Research Officer
National Hellenic Research Foundation (N.H.R.F.)
Institute of Biology, Medicinal Chemistry and Biotechnology
48 Vas. Constantinou Ave., Athens 11635
Greece
--

tel.: +30-210-7273894 <%2B30-210-7273752>
e-mail: kvou...@eie.gr
___
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:
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  http://galaxyproject.org/search/mailinglists/