Re: [galaxy-dev] Rocks cluster; jobs run but Galaxy can't find jobid when submitted via drmaa

[Rémy Dernat]

I forgot to point out the needs of sharing folders and checking the UID/GID
of the galaxy user between your systems (and his access to SGE).

Remy

2016-01-20 16:00 GMT+01:00 Rémy Dernat :

> Hi Eric,
>
> Here we use both solutions: Galaxy and RocksCluster. In Galaxy, you have
> to define your jobs in "config/job_conf.xml" and you should probably source
> a file (search for "environment" in your galaxy.ini) before the submit
> process. In fact, you could have to set a DRMAA_LIBRARY_PATH to load your
> drmaa library; see
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#DRMAA
>
> Best,
> Remy
>
> 2016-01-19 20:28 GMT+01:00 Eric Shell :
>
>> I am trying to get a Galaxy instance running on a Rocks cluster.  I am
>> able to run jobs with the local runner at this point, but I am having an
>> issue with the drmaa runner that I haven't been able to fix.  When I submit
>> a job in Galaxy it is successfully submitted to the cluster and runs to
>> completion according to qacct, but Galaxy just reports "failure running
>> job".
>>
>> Here's what is written to paster.log when I submit a job:
>>
>> 69.181.235.240 - - [19/Jan/2016:11:24:31 -0700] "GET
>>> /api/histories/fb86c918c0d3d33b/contents?dataset_details=bae154fe2294752e%2C6fe732485990d2ac%2C604c4e6e60e997bc%2Cf015f1cb819ec50e%2C9f6f4b3cb6cf43eb%2C3d13d598882b6eb8%2C551006fddcb290ae%2C10b9bbc646c48387%2C7670dfdf35146bc5%2Ce0ec2cf59f1fc79e%2Cee30922e5e4854db%2C9e7a0ba216194210
>>> HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/; "Mozilla/5.0 (Windows NT
>>> 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko)
>>> Chrome/47.0.2526.111 Safari/537.36"
>>> 69.181.235.240 - - [19/Jan/2016:11:24:38 -0700] "GET
>>> /tool_runner/data_source_redirect?tool_id=ucsc_table_direct1 HTTP/1.1" 302
>>> - "https://galaxy.soe.ucsc.edu/; "Mozilla/5.0 (Windows NT 10.0; Win64;
>>> x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111
>>> Safari/537.36"
>>> galaxy.tools.actions.__init__ INFO 2016-01-19 11:24:42,801 Handled
>>> output (327.778 ms)
>>> galaxy.tools.actions.__init__ INFO 2016-01-19 11:24:43,236 Verified
>>> access to datasets (0.023 ms)
>>> galaxy.tools.execute DEBUG 2016-01-19 11:24:43,343 Tool
>>> [ucsc_table_direct1] created job [7019] (919.481 ms)
>>> 69.181.235.240 - - [19/Jan/2016:11:24:42 -0700] "POST /tool_runner
>>> HTTP/1.1" 200 - "https://genome.ucsc.edu/cgi-bin/hgTables; "Mozilla/5.0
>>> (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko)
>>> Chrome/47.0.2526.111 Safari/537.36"
>>> galaxy.jobs DEBUG 2016-01-19 11:24:44,056 (7019) Working directory for
>>> job is: /campusdata/galaxy/galaxy/database/job_working_directory/007/7019
>>> galaxy.jobs.handler DEBUG 2016-01-19 11:24:44,070 (7019) Dispatching to
>>> sge runner
>>> galaxy.jobs DEBUG 2016-01-19 11:24:44,378 (7019) Persisting job
>>> destination (destination id: sge_default)
>>> galaxy.jobs.runners DEBUG 2016-01-19 11:24:44,403 Job [7019] queued
>>> (332.423 ms)
>>> galaxy.jobs.handler INFO 2016-01-19 11:24:44,444 (7019) Job dispatched
>>> 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET /api/genomes
>>> HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/; "Mozilla/5.0 (Windows NT
>>> 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko)
>>> Chrome/47.0.2526.111 Safari/537.36"
>>> 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET
>>> /api/datatypes?extension_only=False& HTTP/1.1" 200 - "
>>> https://galaxy.soe.ucsc.edu/; "Mozilla/5.0 (Windows NT 10.0; Win64;
>>> x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111
>>> Safari/537.36"
>>> 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET
>>> /history/current_history_json HTTP/1.1" 200 - "
>>> https://galaxy.soe.ucsc.edu/; "Mozilla/5.0 (Windows NT 10.0; Win64;
>>> x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111
>>> Safari/537.36"
>>> galaxy.jobs.runners DEBUG 2016-01-19 11:24:46,399 (7019) command is:
>>> python /campusdata/galaxy/galaxy/tools/data_source/data_source.py
>>> /campusdata/galaxy/galaxy/database/files/011/dataset_11361.dat 0;
>>> return_code=$?; python
>>> "/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/set_metadata_IaPURP.py"
>>> "/campusdata/galaxy/galaxy/database/tmp/tmp9Qt0cv"
>>> "/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/galaxy.json"
>>> 

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Peter Cock]

On Wed, Jan 20, 2016 at 2:43 PM, Gildas Le Corguillé
 wrote:
> Hi,
>
> A long time ago, in a far far svn repo, we did this "multiple=true" on Peter
> wrappers.
>
> I will try to propose it quickly :)
>
> Gildas

Great - a pull request against https://github.com/peterjc/galaxy_blast
but if your SVN repo is still online, or you can make a patch/diff file,
we could look at that and try to port the changes. My guess is a lot
of macro work was done in the meantime so it may not be trivial to
repeat your changes :(

Thanks,

Peter
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[galaxy-dev] Data Collection collection_type list:list

[Anmol Hemrom]

Hi,

I was wondering if creating data collection of collection_type="list:list"
is possible?  Because I can see only list, pair and list of pairs options
available.

Why I am asking this question is because I saw this snippet from cuffdiff
tool which includes collection_type="list:list" as below.





Thanks

Anmol
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Re: [galaxy-dev] Data Collection collection_type list:list

[John Chilton]

list:list (as well as list:list:paired, list:list:list, etc...) can be
created via the API or using tools. As an example of the second - if
you had a tool that took in a dataset and split it into a list and
then mapped a list over that tool - Galaxy would produce a list:list
output from the individual jobs. (Explicit framework level support for
grouping a list into a list:list almost made it into 16.01 -
https://github.com/galaxyproject/galaxy/pull/1313 but didn't quite
make the cut, hopefully it will be in 16.04). Tools can also
explicitly produce nested collections such as lists of lists as of PR
#538 (https://github.com/galaxyproject/galaxy/pull/538).

There is however no current GUI or widget support for taking a bunch
of datasets and building a list of lists from them. There was some
discussion on this issue
https://github.com/galaxyproject/galaxy/issues/1312 about adding such
a thing. The builder for a list of pairs is pretty awesome - I imagine
a list of list builder would be a whole new and distinct challenge
unfortunately.

-John


On Wed, Jan 20, 2016 at 4:43 PM, Anmol Hemrom  wrote:
>
> Hi,
>
> I was wondering if creating data collection of collection_type="list:list"
> is possible?  Because I can see only list, pair and list of pairs options
> available.
>
> Why I am asking this question is because I saw this snippet from cuffdiff
> tool which includes collection_type="list:list" as below.
>
> 
>  type="data_collection" collection_type="list:list" />
> 
>
> Thanks
>
> Anmol
>
>
>
>
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Re: [galaxy-dev] Rocks cluster; jobs run but Galaxy can't find jobid when submitted via drmaa

[Eric Shell]

Thanks, Remy.  I went through the cluster documentation and our Rocks
environment seems to be configured properly, after all.

It appears that my issue may be related to the UCSC Main table browser.
The jobs that Galaxy reports have failed are leaving the
job_working_directory behind, with galaxy_#.e error files that contain "The
remote data source application has not sent back a URL parameter in the
request."

[root@campusrocks2 7045]# pwd
/campusdata/galaxy/galaxy/database/job_working_directory/007/7045
[root@campusrocks2 7045]# cat galaxy_7045.e
The remote data source application has not sent back a URL parameter in the
request.

These errors correspond with empty dataset_#.dat files
in /campusdata/galaxy/galaxy/database/files/011/:

[root@campusrocks2 7045]# ll /campusdata/galaxy/galaxy/database/files/011/
-rw-rw-r-- 1 galaxy galaxy0 Jan 20 11:54 dataset_11387.dat

The job failures are intermittent.  Sometimes, a job requesting the exact
same dataset will succeed moments before or after a failed job.  Is there
perhaps a way to tell the table browser to retry when it fails to get the
dataset it is requesting?  Is that even what's going on?

On Wed, Jan 20, 2016 at 7:05 AM, Rémy Dernat  wrote:

> I forgot to point out the needs of sharing folders and checking the
> UID/GID of the galaxy user between your systems (and his access to SGE).
>
> Remy
>
> 2016-01-20 16:00 GMT+01:00 Rémy Dernat :
>
>> Hi Eric,
>>
>> Here we use both solutions: Galaxy and RocksCluster. In Galaxy, you have
>> to define your jobs in "config/job_conf.xml" and you should probably source
>> a file (search for "environment" in your galaxy.ini) before the submit
>> process. In fact, you could have to set a DRMAA_LIBRARY_PATH to load your
>> drmaa library; see
>> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#DRMAA
>>
>> Best,
>> Remy
>>
>> 2016-01-19 20:28 GMT+01:00 Eric Shell :
>>
>>> I am trying to get a Galaxy instance running on a Rocks cluster.  I am
>>> able to run jobs with the local runner at this point, but I am having an
>>> issue with the drmaa runner that I haven't been able to fix.  When I submit
>>> a job in Galaxy it is successfully submitted to the cluster and runs to
>>> completion according to qacct, but Galaxy just reports "failure running
>>> job".
>>>
>>> Here's what is written to paster.log when I submit a job:
>>>
>>> 69.181.235.240 - - [19/Jan/2016:11:24:31 -0700] "GET
 /api/histories/fb86c918c0d3d33b/contents?dataset_details=bae154fe2294752e%2C6fe732485990d2ac%2C604c4e6e60e997bc%2Cf015f1cb819ec50e%2C9f6f4b3cb6cf43eb%2C3d13d598882b6eb8%2C551006fddcb290ae%2C10b9bbc646c48387%2C7670dfdf35146bc5%2Ce0ec2cf59f1fc79e%2Cee30922e5e4854db%2C9e7a0ba216194210
 HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/; "Mozilla/5.0 (Windows
 NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko)
 Chrome/47.0.2526.111 Safari/537.36"
 69.181.235.240 - - [19/Jan/2016:11:24:38 -0700] "GET
 /tool_runner/data_source_redirect?tool_id=ucsc_table_direct1 HTTP/1.1" 302
 - "https://galaxy.soe.ucsc.edu/; "Mozilla/5.0 (Windows NT 10.0; Win64;
 x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111
 Safari/537.36"
 galaxy.tools.actions.__init__ INFO 2016-01-19 11:24:42,801 Handled
 output (327.778 ms)
 galaxy.tools.actions.__init__ INFO 2016-01-19 11:24:43,236 Verified
 access to datasets (0.023 ms)
 galaxy.tools.execute DEBUG 2016-01-19 11:24:43,343 Tool
 [ucsc_table_direct1] created job [7019] (919.481 ms)
 69.181.235.240 - - [19/Jan/2016:11:24:42 -0700] "POST /tool_runner
 HTTP/1.1" 200 - "https://genome.ucsc.edu/cgi-bin/hgTables;
 "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like
 Gecko) Chrome/47.0.2526.111 Safari/537.36"
 galaxy.jobs DEBUG 2016-01-19 11:24:44,056 (7019) Working directory for
 job is: /campusdata/galaxy/galaxy/database/job_working_directory/007/7019
 galaxy.jobs.handler DEBUG 2016-01-19 11:24:44,070 (7019) Dispatching to
 sge runner
 galaxy.jobs DEBUG 2016-01-19 11:24:44,378 (7019) Persisting job
 destination (destination id: sge_default)
 galaxy.jobs.runners DEBUG 2016-01-19 11:24:44,403 Job [7019] queued
 (332.423 ms)
 galaxy.jobs.handler INFO 2016-01-19 11:24:44,444 (7019) Job dispatched
 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET /api/genomes
 HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/; "Mozilla/5.0 (Windows
 NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko)
 Chrome/47.0.2526.111 Safari/537.36"
 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET
 /api/datatypes?extension_only=False& HTTP/1.1" 200 - "
 https://galaxy.soe.ucsc.edu/; "Mozilla/5.0 (Windows NT 10.0; Win64;
 x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111
 Safari/537.36"
 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET
 

Re: [galaxy-dev] Running Galaxy jobs remotely via ssh / rsh

[John Chilton]

Even if you just have two servers, I would strongly recommend you
setup a cluster distributed resource manager (DRM) like SLURM, PBS, or
Condor and ensuring there exists a shared file system between Galaxy
and the node running the jobs. You wouldn't even need to use the CLI
job runner - you could just use the DRMAA job runner directly in most
cases if you configured one of these - which is what most people use
to run Galaxy jobs across machines on a cluster.

If you wish to send Galaxy jobs to a single machine without setting up
a DRM or if a shared file system is impossible - you can use Pulsar
(http://pulsar.readthedocs.org/en/latest/) for most kinds of jobs
(some jobs like data source jobs and upload jobs should remain on the
Galxay host in a such a configuration).

-John

On Wed, Jan 20, 2016 at 5:18 PM, D K  wrote:
> Hi,
>
> I would like to run the Galaxy framework on server A, while performing all
> of the jobs on server B using ssh.
>
> Looking at the documentation here:
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CLI, this
> seems like it should be possible. However, the documentation states that the
> cli runner requires, at a minimum, two parameters, one for the shell (which
> I'm selecting SecureShell) and a Job plugin. I'm not sure what this should
> be since the ones available are Torque, Slurm, and SlurmTorque and I'm not
> running any of these. Can anyone give me any hints? My current job_conf.xml
> looks like this:
>
> 
> 
> 
> 
>  load="galaxy.jobs.runners.cli:ShellJobRunner"/>
> 
> 
> 
> 
> 
> 
>SecureShell
>cli
>computehost
>galaxy
> 
> 
> 
>
>
> As an alternative, in a tool xml I tried directly sshing between the
>  tags e.g.:
>
>   ssh galaxy@serverB 'sh $__tool_directory__/runTool.sh --verbose >
> $output 2>1' 
>
> This appears to work. Is it possible to "inject" this ssh command into tool
> execution in Galaxy?
>
> I was looking to do this to avoid having to install a scheduler like SGE or
> using Pulsar. Any suggestions would be greatly appreciated.
>
> Thanks!
>
>
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Re: [galaxy-dev] Sample tracking / external services - still supported?

[Langhorst, Brad]

Hi Matthias:

I think it’s abandoned, I’ve tried to use it with no success.

I think it should be brought up to date or be removed to save people from 
wasting time trying to get it working.


Brad 

--
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs

> On Jan 20, 2016, at 3:06 AM, Matthias De Smet  
> wrote:
> 
> Hi all,
> 
> Is there still any support out there for sample tracking / data transfers 
> from sequencer / external services? Or is this part of Galaxy completely 
> abandoned/deprecated? All the info in the wiki or other sources is at least 5 
> years old or refers to files and code that isn’t there anymore.
> 
> Any help?
> 
> Thanks!
> 
> Matthias
> 
> 
> 
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Peter Cock]

On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD
 wrote:
> Hi,
>
> I would like to add some tools of the EMBOSS suite (6.6.0) to my Galaxy
> instance. It seems that the only wrapper available for Galaxy is for the
> 5.0.0 version
> (http://dev.list.galaxyproject.org/Galaxy-with-EMBOSS-5-or-EMBOSS-6-td4658043.html).
>
> I would like to know if someone has already tried (successfully or not) to
> wrap this tools base on the old wrappers to estimate the workload that
> awaits me (for prettyseq and water mostly).

There is work in progress here, see:
https://github.com/galaxyproject/tools-iuc/issues/65
https://github.com/galaxyproject/tools-iuc/pull/131

Have you compared the API options to see if anything changed
here in EMBOSS? I don't recall any major changes to water,
but I don't use prettyseq at all.

> Could there be an invalid datatype format for example ?

Many datatypes were already defined for the EMBOSS 5.0.0
wrappers, so that is less likely to be a problem for EMBOSS 6.6.0

> I have another question regarding the NCBI BLAST+ suite : is there a way to
> edit the XML file to enable the selection of multiple databases as proposed
> by the command lines tool ?

Possible by editing the wrappers, yes. However it will likely break
if any of the paths have spaces in them due to the NCBI wanting
a space separated list of database paths - a potential problem
already in the makeblastdb wrapper.

Are you wanting to use multiple databases from the *.loc files at
once, multiple databases from the current history, or both? Please
log this as an enhancement request here:

https://github.com/peterjc/galaxy_blast/issues

Thanks,

Peter
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[galaxy-dev] Ansible roles: galaxy_server_dir vs galaxy_home_dir and galaxy_root

[Peter van Heusden]

Hi there

We've just finished provisioning a new Galaxy server here using the
ansible-galaxy and ansible-galaxy-extras roles, with some extra roles from
Nate and our own creation. In the ansible-galaxy role Galaxy's install
location is set using the galaxy_server_dir variable, but in
ansible-galaxy-extras the variables galaxy_home_dir and galaxy_root
(presumably for distinct locations for the galaxy user's home directory and
the root of the Galaxy installation) are used.

Is this difference deliberate? Attached is our Ansible playbook - we just
configured the variables to all point to the same location (and set the
galaxy_venv_dir to be .venv not venv). I thought the two roles were meant
to work together, so this difference is somewhat confusing.

Thanks,
Peter


galaxydev.yml
Description: application/yaml
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[galaxy-dev] Galaxy sending jobs to multiple clusters

[Nikolay Aleksandrov Vazov]

Hi, John, Dan, Carrie and all others,


I am considering a task of setting up a Galaxy instance which shall send jobs 
to more than on cluster at a time. In my case I am using drmaa-python and I was 
wondering if it was possible to configure multiple drmaa runners each 
"pointing" at a different (slurm) control host, e.g.


local

drmaa1

drmaa2


Thanks a lot for your advice


Nikolay



===
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo
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[galaxy-dev] RedHat versus CentOs

[Hans-Rudolf Hotz]

Dear All

Our production Galaxy server has been running smoothly on a single 
multicore box with Red Hat 6.7. As this box gets older and older, it is 
in now time to replace it.


At the same time, we are also considering switching the operating system 
to CentOS 7. Has anyone switched a production installation from Red Hat 
to CentOS ?


'Galaxy Main' is running on CentOS, isn't-it?

I am also interested in plain numbers: how many of you are using Red 
Hat, how many CentOS and which version for your production server. I 
will probably need such numbers to convince our IT department.


There is no need to reply to the mailing list, just reply to me 
(h...@fmi.ch) and if I get enough I will then collate and anonymize all 
the data and post back. Maybe we can even add such information to the 
wiki (https://wiki.galaxyproject.org/Community/Deployments)?



Thank you very much for your help
Hans-Rudolf


--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Peter Cock]

On Wed, Jan 20, 2016 at 2:22 PM, Floreline TOUCHARD
 wrote:
> Thanks for the answer !
>
> I compared the two versions of tools. It does not seem to be any major
> differences indeed. I added these tools to my instance successfully.

Great :)

> Additional options in version 6 are not to be integrate to my Galaxy
> instance immediately. I will update my XML file later if need arises. The
> old wrappers are perfect for the moment.

If you have any feedback on the IUC work, please comment on the
GitHub issue.

> For the NCBI BLAST+ suite I would like to select multiple databases only
> from the *.loc files. There is no spaces in the paths in my *.loc files
> (however there is spaces in the names of these databases, but I guess this
> is not a problem). I thought I just have to add a tag "multiple=true" in the
> XML file but it seems a bit more complex. Am I missing something ?

As far as I know, the multiple="true" tag only works on input datasets
from your history. But that would make sense... I don't think I have
ever tried this.

Even if that worked, the  tag would also need modifying
to account for the multiple values from db_opts.database.

Another potential option is to extend makeblastdb which can in
principle combine multiple FASTA and pre-existing databases...

Peter
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Re: [galaxy-dev] Sample tracking / external services - still supported?

[Martin Čech]

Hello Matthias,

As you correctly identified the original implementation, in spite of being
present in the Galaxy distribution, is treated as deprecated.
However I know about three sample tracking implementation based on Galaxy's
old sample tracking.


   - *TRON Mainz*
   http://bioinformatics.oxfordjournals.org/content/29/9/1233.longsource
   here: https://bitbucket.org/jelle/galaxy-central-tron-lims
   - *Massachusetts General Hospital *
   
http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/
source here:https://bitbucket.org/chapmanb/galaxy-central
   - https://github.com/specimentracking


I am not sure about the current state of the first two but the last one is
being used in a pilot project for tracking using smartphones and QR codes
here at PSU and is under our somewhat active development.

Let me know if you have more questions.
Thanks for using Galaxy.

Martin

On Wed, Jan 20, 2016 at 3:06 AM Matthias De Smet 
wrote:

> Hi all,
>
> Is there still any support out there for sample tracking / data transfers
> from sequencer / external services? Or is this part of Galaxy completely
> abandoned/deprecated? All the info in the wiki or other sources is at least
> 5 years old or refers to files and code that isn’t there anymore.
>
> Any help?
>
> Thanks!
>
> Matthias
>
>
>
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Gildas Le Corguillé]

Hi,

A long time ago, in a far far svn repo, we did this "multiple=true" on Peter 
wrappers.

I will try to propose it quickly :)

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 20 janv. 2016 à 15:37, Peter Cock  a écrit :
> 
> On Wed, Jan 20, 2016 at 2:22 PM, Floreline TOUCHARD
>  wrote:
>> Thanks for the answer !
>> 
>> I compared the two versions of tools. It does not seem to be any major
>> differences indeed. I added these tools to my instance successfully.
> 
> Great :)
> 
>> Additional options in version 6 are not to be integrate to my Galaxy
>> instance immediately. I will update my XML file later if need arises. The
>> old wrappers are perfect for the moment.
> 
> If you have any feedback on the IUC work, please comment on the
> GitHub issue.
> 
>> For the NCBI BLAST+ suite I would like to select multiple databases only
>> from the *.loc files. There is no spaces in the paths in my *.loc files
>> (however there is spaces in the names of these databases, but I guess this
>> is not a problem). I thought I just have to add a tag "multiple=true" in the
>> XML file but it seems a bit more complex. Am I missing something ?
> 
> As far as I know, the multiple="true" tag only works on input datasets
> from your history. But that would make sense... I don't think I have
> ever tried this.
> 
> Even if that worked, the  tag would also need modifying
> to account for the multiple values from db_opts.database.
> 
> Another potential option is to extend makeblastdb which can in
> principle combine multiple FASTA and pre-existing databases...
> 
> Peter
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Floreline TOUCHARD]

Thanks for the answer !

I compared the two versions of tools. It does not seem to be any major
differences indeed. I added these tools to my instance successfully.
Additional options in version 6 are not to be integrate to my Galaxy
instance immediately. I will update my XML file later if need arises. The
old wrappers are perfect for the moment.

For the NCBI BLAST+ suite I would like to select multiple databases
only from the *.loc files. There is no spaces in the paths in my *.loc
files (however there is spaces in the names of these databases, but I guess
this is not a problem). I thought I just have to add a tag "multiple=true"
in the XML file but it seems a bit more complex. Am I missing something ?

F.T


2016-01-20 10:33 GMT+01:00 Peter Cock :

> On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD
>  wrote:
> > Hi,
> >
> > I would like to add some tools of the EMBOSS suite (6.6.0) to my Galaxy
> > instance. It seems that the only wrapper available for Galaxy is for the
> > 5.0.0 version
> > (
> http://dev.list.galaxyproject.org/Galaxy-with-EMBOSS-5-or-EMBOSS-6-td4658043.html
> ).
> >
> > I would like to know if someone has already tried (successfully or not)
> to
> > wrap this tools base on the old wrappers to estimate the workload that
> > awaits me (for prettyseq and water mostly).
>
> There is work in progress here, see:
> https://github.com/galaxyproject/tools-iuc/issues/65
> https://github.com/galaxyproject/tools-iuc/pull/131
>
> Have you compared the API options to see if anything changed
> here in EMBOSS? I don't recall any major changes to water,
> but I don't use prettyseq at all.
>
> > Could there be an invalid datatype format for example ?
>
> Many datatypes were already defined for the EMBOSS 5.0.0
> wrappers, so that is less likely to be a problem for EMBOSS 6.6.0
>
> > I have another question regarding the NCBI BLAST+ suite : is there a way
> to
> > edit the XML file to enable the selection of multiple databases as
> proposed
> > by the command lines tool ?
>
> Possible by editing the wrappers, yes. However it will likely break
> if any of the paths have spaces in them due to the NCBI wanting
> a space separated list of database paths - a potential problem
> already in the makeblastdb wrapper.
>
> Are you wanting to use multiple databases from the *.loc files at
> once, multiple databases from the current history, or both? Please
> log this as an enhancement request here:
>
> https://github.com/peterjc/galaxy_blast/issues
>
> Thanks,
>
> Peter
>
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