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.
On 22 February 2015 at 23:17, Michael Thon <mike.thon@gmail.com> 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
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 <saketkc@gmail.com> wrote:
On 22 February 2015 at 23:17, Michael Thon <mike.thon@gmail.com> 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
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 <saketkc@gmail.com> wrote:
On 22 February 2015 at 23:17, Michael Thon <mike.thon@gmail.com> 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
On Feb 23, 2015, at 8:23 AM, Saket Choudhary <saketkc@gmail.com> wrote:
On 22 February 2015 at 23:17, Michael Thon <mike.thon@gmail.com> 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...
On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon <mike.thon@gmail.com> 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
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 <p.j.a.cock@googlemail.com> wrote:
On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon <mike.thon@gmail.com> 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/
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 <jmchilton@gmail.com> 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 <p.j.a.cock@googlemail.com> wrote:
On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon <mike.thon@gmail.com> 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/
On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon <mike.thon@gmail.com> 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
Am 24.02.2015 um 10:03 schrieb Peter Cock:
On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon <mike.thon@gmail.com> 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 ___________________________________________________________ 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/
On Tue, Feb 24, 2015 at 9:19 AM, Björn Grüning <bjoern.gruening@gmail.com> 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
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/
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/
participants (6)
-
Björn Grüning -
John Chilton -
Michael Thon -
Nicola Soranzo -
Peter Cock -
Saket Choudhary