Unable to upload bam files as links to my local galaxy instance - please help!

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Unable to upload bam files as links to my local galaxy instance - please help!

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 <module>
    __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 <command> [options]

Command: view        SAM<->BAM conversion
         sort        sort alignment file
         mpileup     multi-way pileup
         depth       compute the depth
         faidx       index/extract FASTA
         tview       text alignment viewer
         index       index alignment
         idxstats    BAM index stats (r595 or later)
         fixmate     fix mate information
         flagstat    simple stats
         calmd       recalculate MD/NM tags and '=' bases
         merge       merge sorted alignments
         rmdup       remove PCR duplicates
         reheader    replace 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.: <a href="tel:%2B30-210-7273752" value="+302107273752" target="_blank">+30-210-7273894
e-mail: [hidden email]

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

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 <[hidden email]> 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
> <module>
>     __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 <command> [options]
>
> Command: view        SAM<->BAM conversion
>          sort        sort alignment file
>          mpileup     multi-way pileup
>          depth       compute the depth
>          faidx       index/extract FASTA
>          tview       text alignment viewer
>          index       index alignment
>          idxstats    BAM index stats (r595 or later)
>          fixmate     fix mate information
>          flagstat    simple stats
>          calmd       recalculate MD/NM tags and '=' bases
>          merge       merge sorted alignments
>          rmdup       remove PCR duplicates
>          reheader    replace 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: [hidden email]
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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