tophat error

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tophat error

Michael Thon
I have a local installation of galaxy on my server.  When I run tophat2, the job runs but then throws this error:
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1107, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )  # call datatype.set_meta directly for the initial set_meta call during dataset creation
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 250, in set_meta
    raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: Samtools-htslib-API: bam_index_build2() not yet implemented
Aborted (core dumped)

Any advice would be appreciated.


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Re: tophat error

saketkc
On 22 February 2015 at 23:17, Michael Thon <[hidden email]> wrote:
> bam_index_build2() not yet

Hi Michael,

This seems to be related to this:
https://github.com/samtools/samtools/issues/199

You should probably switch to samtools 0.1.19

Saket
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Re: tophat error

Michael Thon
Hi - Thanks for the info.  I had two versions of samtools installed so I uninstalled one and left only samtools 0.1.19 however I still get the error.  I'm using the tophat2 tool and I'm still getting the error.  I just reinstalled the tophat2 tool and I'm running it again.


> On Feb 23, 2015, at 8:23 AM, Saket Choudhary <[hidden email]> wrote:
>
> On 22 February 2015 at 23:17, Michael Thon <[hidden email]> wrote:
>> bam_index_build2() not yet
>
> Hi Michael,
>
> This seems to be related to this:
> https://github.com/samtools/samtools/issues/199
>
> You should probably switch to samtools 0.1.19
>
> Saket

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Re: tophat error

Michael Thon
In reply to this post by saketkc
Nope, it still isn't working. I deleted tophat2, package_tophat2 and package_samtools and then reinstalled tophat2 from Galaxy main. Here are what I think are the relevant installed packages:

tophat2
package_tophat2_2_0_9
package_samtools_0_1_18

Any other advice would be appreciated.

> On Feb 23, 2015, at 8:23 AM, Saket Choudhary <[hidden email]> wrote:
>
> On 22 February 2015 at 23:17, Michael Thon <[hidden email]> wrote:
>> bam_index_build2() not yet
>
> Hi Michael,
>
> This seems to be related to this:
> https://github.com/samtools/samtools/issues/199
>
> You should probably switch to samtools 0.1.19
>
> Saket

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Re: tophat error

Michael Thon
In reply to this post by saketkc

On Feb 23, 2015, at 8:23 AM, Saket Choudhary <[hidden email]> wrote:

On 22 February 2015 at 23:17, Michael Thon <[hidden email]> wrote:
bam_index_build2() not yet

Hi Michael,

This seems to be related to this:
https://github.com/samtools/samtools/issues/199

You should probably switch to samtools 0.1.19

Saket

I figured that galaxy must be finding a samtools v1.1 even though the tool was not installed, according to the admin page. I uninstalled the samtools that was installed system-wide on the server.  Now I get this error:
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1107, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )  # call datatype.set_meta directly for the initial set_meta call during dataset creation
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 250, in set_meta
    raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
So, galaxy is not using the samtools from the installed galaxy package and is instead using the system one.  I'll try to reinstall samtools and see if that fixes it...




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Re: tophat error

Peter Cock
On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon <[hidden email]> wrote:

>
> I figured that galaxy must be finding a samtools v1.1 even though the tool
> was not installed, according to the admin page. I uninstalled the samtools
> that was installed system-wide on the server.  Now I get this error:
>
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
> 129, in queue_job
>     job_wrapper.finish( stdout, stderr, exit_code )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1107, in
> finish
>     dataset.datatype.set_meta( dataset, overwrite=False )  # call
> datatype.set_meta directly for the initial set_meta call during dataset
> creation
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 250,
> in set_meta
>     raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
>
> So, galaxy is not using the samtools from the installed galaxy package and
> is instead using the system one.  I'll try to reinstall samtools and see if
> that fixes it...

In this case Galaxy itself expects samtools on the $PATH for managing
BAM files separately from which ever tool you are using within Galaxy.

The Galaxy Tool Shed dependencies are on a per-tool basis, and not
used by Galaxy itself.

This ought to be on the wiki somewhere, but I failed to find it...

Peter
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Re: tophat error

John Chilton-4
Sorry for this messy situation. With the next release Galaxy will be
able to set metadata using any version of samtools due to an excellent
fix by Nate - so this hopefully will become less of an issue.

-John

On Mon, Feb 23, 2015 at 10:01 AM, Peter Cock <[hidden email]> wrote:

> On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon <[hidden email]> wrote:
>>
>> I figured that galaxy must be finding a samtools v1.1 even though the tool
>> was not installed, according to the admin page. I uninstalled the samtools
>> that was installed system-wide on the server.  Now I get this error:
>>
>> Traceback (most recent call last):
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
>> 129, in queue_job
>>     job_wrapper.finish( stdout, stderr, exit_code )
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1107, in
>> finish
>>     dataset.datatype.set_meta( dataset, overwrite=False )  # call
>> datatype.set_meta directly for the initial set_meta call during dataset
>> creation
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 250,
>> in set_meta
>>     raise Exception, "Error Setting BAM Metadata: %s" % stderr
>> Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
>>
>> So, galaxy is not using the samtools from the installed galaxy package and
>> is instead using the system one.  I'll try to reinstall samtools and see if
>> that fixes it...
>
> In this case Galaxy itself expects samtools on the $PATH for managing
> BAM files separately from which ever tool you are using within Galaxy.
>
> The Galaxy Tool Shed dependencies are on a per-tool basis, and not
> used by Galaxy itself.
>
> This ought to be on the wiki somewhere, but I failed to find it...
>
> Peter
> ___________________________________________________________
> 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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Re: tophat error

Michael Thon
The main problem for me was that I was not aware that the tophat tool had a dependency on a command line tool outside of galaxy installation.  I see in the admin interface that tophat has a dependency on samtools of type package and I assumed that should provide the samtools binary.  Of course I have not read the manuals regarding tool sheds, dependencies, etc so thats probably where my problem started in the first place...


> On Feb 24, 2015, at 3:18 AM, John Chilton <[hidden email]> wrote:
>
> Sorry for this messy situation. With the next release Galaxy will be
> able to set metadata using any version of samtools due to an excellent
> fix by Nate - so this hopefully will become less of an issue.
>
> -John
>
> On Mon, Feb 23, 2015 at 10:01 AM, Peter Cock <[hidden email]> wrote:
>> On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon <[hidden email]> wrote:
>>>
>>> I figured that galaxy must be finding a samtools v1.1 even though the tool
>>> was not installed, according to the admin page. I uninstalled the samtools
>>> that was installed system-wide on the server.  Now I get this error:
>>>
>>> Traceback (most recent call last):
>>>  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
>>> 129, in queue_job
>>>    job_wrapper.finish( stdout, stderr, exit_code )
>>>  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1107, in
>>> finish
>>>    dataset.datatype.set_meta( dataset, overwrite=False )  # call
>>> datatype.set_meta directly for the initial set_meta call during dataset
>>> creation
>>>  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 250,
>>> in set_meta
>>>    raise Exception, "Error Setting BAM Metadata: %s" % stderr
>>> Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
>>>
>>> So, galaxy is not using the samtools from the installed galaxy package and
>>> is instead using the system one.  I'll try to reinstall samtools and see if
>>> that fixes it...
>>
>> In this case Galaxy itself expects samtools on the $PATH for managing
>> BAM files separately from which ever tool you are using within Galaxy.
>>
>> The Galaxy Tool Shed dependencies are on a per-tool basis, and not
>> used by Galaxy itself.
>>
>> This ought to be on the wiki somewhere, but I failed to find it...
>>
>> Peter
>> ___________________________________________________________
>> 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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Re: tophat error

Peter Cock
On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon <[hidden email]> wrote:
> The main problem for me was that I was not aware that the tophat
> tool had a dependency on a command line tool outside of galaxy
> installation.  I see in the admin interface that tophat has a dependency
> on samtools of type package and I assumed that should provide the
> samtools binary.  Of course I have not read the manuals regarding
> tool sheds, dependencies, etc so thats probably where my problem
> started in the first place...

I can see your chain of thought here. Unfortunately while the tophat
tool (or any tool) may explicitly use samtools (and request a particular
version via the dependencies system), once the tool has finished it
has produced a BAM file. So far so good, but at that point Galaxy
tries to index the BAM file itself. This happens for any BAM file,
regardless of the tool which created it - and simply expects samtools
on the $PATH.

If this is on the wiki (core dependencies of Galaxy itself), could
someone post the URL here please?

Peter
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Re: tophat error

Björn Grüning-3


Am 24.02.2015 um 10:03 schrieb Peter Cock:

> On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon <[hidden email]> wrote:
>> The main problem for me was that I was not aware that the tophat
>> tool had a dependency on a command line tool outside of galaxy
>> installation.  I see in the admin interface that tophat has a dependency
>> on samtools of type package and I assumed that should provide the
>> samtools binary.  Of course I have not read the manuals regarding
>> tool sheds, dependencies, etc so thats probably where my problem
>> started in the first place...
>
> I can see your chain of thought here. Unfortunately while the tophat
> tool (or any tool) may explicitly use samtools (and request a particular
> version via the dependencies system), once the tool has finished it
> has produced a BAM file. So far so good, but at that point Galaxy
> tries to index the BAM file itself. This happens for any BAM file,
> regardless of the tool which created it - and simply expects samtools
> on the $PATH.
>
> If this is on the wiki (core dependencies of Galaxy itself), could
> someone post the URL here please?

It is not listed here:
https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList

I can be wrong but I think Galaxy will search in
<galaxy-tools>/samtools/default if samtools is not on your $PATH.

Can anyone confirm this?

Ciao,
Bjoern

> Peter
> ___________________________________________________________
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>
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Re: tophat error

Peter Cock
On Tue, Feb 24, 2015 at 9:19 AM, Björn Grüning
<[hidden email]> wrote:

> Am 24.02.2015 um 10:03 schrieb Peter Cock:
>> ... So far so good, but at that point Galaxy
>> tries to index the BAM file itself. This happens for any BAM file,
>> regardless of the tool which created it - and simply expects samtools
>> on the $PATH.
>>
>> If this is on the wiki (core dependencies of Galaxy itself), could
>> someone post the URL here please?
>
> It is not listed here:
> https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList

Yes, that page is about dependencies of add-on tools (things
that existing or new tools may assume are installed).

In this case samtools is expected by the Galaxy core (not a tool).
What else falls into this set of dependencies?

> I can be wrong but I think Galaxy will search in
> <galaxy-tools>/samtools/default if samtools is not on your $PATH.
>
> Can anyone confirm this?
>
> Ciao,
> Bjoern

I don't know, sorry.

Peter
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Re: tophat error

Nicola Soranzo-2
In reply to this post by Björn Grüning-3
Il 24.02.2015 10:19 Björn Grüning ha scritto:

> Am 24.02.2015 um 10:03 schrieb Peter Cock:
>
>> On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote:
>>
>>> The main problem for me was that I was not aware that the tophat
>>> tool
>>> had a dependency on a command line tool outside of galaxy
>>> installation. I see in the admin interface that tophat has a
>>> dependency on samtools of type package and I assumed that should
>>> provide the samtools binary. Of course I have not read the manuals
>>> regarding tool sheds, dependencies, etc so thats probably where my
>>> problem started in the first place...
>> I can see your chain of thought here. Unfortunately while the tophat
>> tool (or any tool) may explicitly use samtools (and request a
>> particular version via the dependencies system), once the tool has
>> finished it has produced a BAM file. So far so good, but at that
>> point
>> Galaxy tries to index the BAM file itself. This happens for any BAM
>> file, regardless of the tool which created it - and simply expects
>> samtools on the $PATH. If this is on the wiki (core dependencies of
>> Galaxy itself), could someone post the URL here please?
>
> It is not listed here:
> https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList
>
> I can be wrong but I think Galaxy will search in/samtools/default if
> samtools is not on your $PATH.
>
> Can anyone confirm this?

Galaxy should search first in <tool_dependencies_dir>/samtools/default/
(where <tool_dependencies_dir> is what you have configured in the
tool_dependency_dir directive of config/galaxy.ini), then in $PATH .

Best,
Nicola


Connetti gratis il mondo con la nuova indoona:  hai la chat, le
chiamate, le video chiamate e persino le chiamate di gruppo.
E chiami gratis anche i numeri fissi e mobili nel mondo!
Scarica subito l’app Vai su https://www.indoona.com/


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Re: tophat error

Björn Grüning-3


Am 24.02.2015 um 13:01 schrieb Nicola Soranzo:

> Il 24.02.2015 10:19 Björn Grüning ha scritto:
>
>> Am 24.02.2015 um 10:03 schrieb Peter Cock:
>>
>>> On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote:
>>>
>>>> The main problem for me was that I was not aware that the tophat tool
>>>> had a dependency on a command line tool outside of galaxy
>>>> installation. I see in the admin interface that tophat has a
>>>> dependency on samtools of type package and I assumed that should
>>>> provide the samtools binary. Of course I have not read the manuals
>>>> regarding tool sheds, dependencies, etc so thats probably where my
>>>> problem started in the first place...
>>> I can see your chain of thought here. Unfortunately while the tophat
>>> tool (or any tool) may explicitly use samtools (and request a
>>> particular version via the dependencies system), once the tool has
>>> finished it has produced a BAM file. So far so good, but at that point
>>> Galaxy tries to index the BAM file itself. This happens for any BAM
>>> file, regardless of the tool which created it - and simply expects
>>> samtools on the $PATH. If this is on the wiki (core dependencies of
>>> Galaxy itself), could someone post the URL here please?
>>
>> It is not listed here:
>> https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList
>>
>> I can be wrong but I think Galaxy will search in/samtools/default if
>> samtools is not on your $PATH.
>>
>> Can anyone confirm this?
>
> Galaxy should search first in <tool_dependencies_dir>/samtools/default/
> (where <tool_dependencies_dir> is what you have configured in the
> tool_dependency_dir directive of config/galaxy.ini), then in $PATH .

Great thanks Nicola!
Bjoern

> Best,
> Nicola
>
>
> Connetti gratis il mondo con la nuova indoona:  hai la chat, le
> chiamate, le video chiamate e persino le chiamate di gruppo.
> E chiami gratis anche i numeri fissi e mobili nel mondo!
> Scarica subito l’app Vai su https://www.indoona.com/
>
>
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