[galaxy-dev] Output file permissions different pbs:/// VS local:/// job runners

[Rob Syme]

Hi all.

When I run the FastQC tool using the default local job runner, it produces
a folder of files with permission 664:

-rw-rw-r-- 1 galaxy galaxy  17K Jul  5 17:29 duplication_levels.png
-rw-rw-r-- 1 galaxy galaxy 1.6K Jul  5 17:29 error.png
-rw-rw-r-- 1 galaxy galaxy 7.5K Jul  5 17:29 fastqc_data.txt


When I switch to using the(local) pbs queue, it produces a folder with
permissions 600:

-rw--- 1 galaxy galaxy  15K Jul  6 09:10 duplication_levels.png
-rw--- 1 galaxy galaxy 1.6K Jul  6 09:10 error.png
-rw--- 1 galaxy galaxy 8.8K Jul  6 09:10 fastqc_data.txt


The final dat file (in database/files/000/dataset_xx.dat) is fine, it's
just the files in the corresponding folder
(database/files/000/dataset_xx_files/*) that have the incorrect permissions.
These more restrictive permissions mean that the files cannot be read by
apache, resulting a bunch of broken links when viewing the tool's output.

Does anybody know why this might be happening or how to resolve it?

Many thanks.

-r
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[galaxy-dev] Galaxy cleaning up after it self after jobs fail

[Anthonius deBoer]

I am running galaxy on a system that normally runs all jobs on the cluster, but some jobs need to be run locally...But when I restart galaxy when these jobs are running, those jobs fail (and I am fine with that)...But then when I check the logs, I see a lot of this kind of errors and the word CRITICAL scares me a little...It complains about certain directories not being empty (although they look empty to me when I look at them)But if it needs to clean up should it not expect stuff to be in those working directories? And why is this a critical error and why don't those directories get removed anyway...It clutters my database and I fear this was the reason for weird behaviour I saw earlier, since it may re-use some of these directories after a while ?galaxy.objectstore CRITICAL 2012-07-05 16:57:24,964 /mnt/ngs/analysis/tdeboer/galaxy-data/database2/job_working_directory/003/3350 delete error [Errno 39] Directory not empty: '/mnt/ngs/analysis/tdeboer/galaxy-data/database2/job_working_directory/003/3350'ThanksThon___
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Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

[Anthonius deBoer]

OK...I tried this and it no longer removes the entries from the history...Thanks!I do see that each of the new histories I create still have a reference to some of the other files I pick up from the library (such as dbSNP) but those entries in the history have the number "None" in stead of the usual 1,2 3 etc. that each file in a history hasI guess that is an artifact and it does not really bother me, although it makes it hard to run a tool again that uses one of those files later manually, but since that is not the point of running through the API it is fine for now, but it just looks scary...ThonOn Jul 05, 2012, at 02:34 PM, Dannon Baker  wrote:On Jul 5, 2012, at 5:33 PM, Thon Deboer wrote: > data['no_add_to_history']="True" ?  Should do it. ___
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[galaxy-dev] Has anyone implemented PINDEL as a tool in their GALAXY

[Anthonius deBoer]

Hi,I am about to embark of embedding PINDEL into GALAXY since it is not available in the TOOLSHED.Before I do, I thought I check if someone has already done this and could send me their XML so I don't have to start from scratch...Thanks!Thon
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Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

[Ann Black-Ziegelbein]

For anyone :) Please join us on Monday -

Thanks,

Ann

On 7/5/2012 4:15 PM, Thon Deboer wrote:

Is this conference open for anyone or just (self appointed?) Czars? :)
Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839
thondeb...@me.com 
LinkedIn Profile 




On Jun 28, 2012, at 2:14 AM, Sebastian Schaaf wrote:


Also hello to everyone,

As I browsed through those tabs which are open for weeks I 
rediscovered the online survey "Interested in Deploying Your Own 
Local Galaxy?" connected to this thread here. The last response I 
could find in this context was the one below which was written by Ann.
To make it short: did anything happen in the meantime, has there been 
any telephone conference, is there still any interest out there? I 
filled out the survey and ask myself wether it makes still sense to 
submit the form. Regarding the fact I can participate in this year's 
Galaxy Developers Conference (GCC in Chicago) I would be quite happy 
if some contacts may arise from this thread or the conference or both 
in a mutual way (which would be somewhat perfect). The heavily 
discussed topic regarding time zones should not prevent us from going 
ahead.


Best regards and thanks in advance,

Sebastian Schaaf
(Munich, Germany)


Ann Black-Ziegelbein schrieb:

Hello everyone!

Here is a link to a brief survey about how you are using, or plan to 
use Galaxy locally.  If you could take a moment to complete the 
survey, it will help steer the teleconferences as we get going (and 
also alleviate having to spend time on the call providing the same 
background info).  The results of the survey will be made public off 
of a new wiki site that Galaxy's Dave Clements is arranging for the 
group - thanks Dave!


Web Survey: 
https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ


Once the teleconference infrastructure details are in place and 
finalized, I will send out a web poll to see if we can find a time 
that works for the majority.


Thanks,

Ann Black-Ziegelbein



On 4/27/2012 2:14 PM, Ryan Golhar wrote:

This is a great idea.

On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein 
mailto:annbl...@eng.uiowa.edu> 
> wrote:


   Hi everyone -

   Here at the University of Iowa we are working on deploying Galaxy
   locally for campus wide access.  I am interested in forming a
   community of other institutions trying to deploy Galaxy locally
   and mange/operate it on a broad level.  Is anyone else?   If
   there is enough interest, possibly we could have  a community
   conference call every other month to have an open discussion on
   how we are all deploying galaxy, customizations we are making,
   problems we are encountering, bugs, and any add-on operations
   management for galaxy being developed, etc.

   Would love to hear from others operating Galaxy or in process of
   standing up a local deployment.

   Thanks!

   Ann Black-Ziegelbein
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--
Sebastian Schaaf, M.Sc. Bioinformatics
Chair of Biometry and Bioinformatics
Department of Medical Information Sciences, Biometry and Epidemiology
University of Munich
Marchioninistr. 15, K U1 (postal)
Marchioninistr. 17, U 006 (office)
D-81377 Munich (Germany)
Tel: +49 89 2180-78229

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Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

[Dannon Baker]

On Jul 5, 2012, at 5:40 PM, Anthonius deBoer wrote:
> WOW...I guess I know how you guys that designed the API think :)
> 
> Small other question...Is it possible (yet) to pass a parameter to the API 
> yet, that is NOT an input step?
> Things that get defined in the workflow step such as {Analysis_Run} that get 
> filled in at runtime?
> Now it reverts to "X__oc__Analysis_Run__cc__" but I would like to change this 
> at runtime through the API...

Not yet.  If I remember correctly, the tool API currently allows this (passing 
a dictionary of parameters to the tool at runtime), and it's definitely the 
plan that the functionality will eventually be available from the workflow API 
as well.

-Dannon
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Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

[Anthonius deBoer]

WOW...I guess I know how you guys that designed the API think :)Small other question...Is it possible (yet) to pass a parameter to the API yet, that is NOT an input step?Things that get defined in the workflow step such as {Analysis_Run} that get filled in at runtime?Now it reverts to "X__oc__Analysis_Run__cc__" but I would like to change this at runtime through the API...ThanksThonOn Jul 05, 2012, at 02:34 PM, Dannon Baker  wrote:On Jul 5, 2012, at 5:33 PM, Thon Deboer wrote: > data['no_add_to_history']="True" ?  Should do it. 
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Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

[Dannon Baker]

On Jul 5, 2012, at 5:33 PM, Thon Deboer wrote:
> data['no_add_to_history']="True" ?

Should do it.

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Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

[Thon Deboer]

Thanks for the fast reply...

How do I add this to the "payload"?

Is it part of ds_map or something else?

data['workflow_id'] = 
data['history'] = 
data['ds_map'] = {}

data['no_add_to_history']="True" ?

or is it part of the actual definition of the input step?

Thanks

Thon

Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839
thondeb...@me.com
LinkedIn Profile




On Jul 5, 2012, at 2:12 PM, Thon Deboer wrote:

> Hi,
> 
> I am continueing to struggle with the API
> 
> I have created a workflow execution engine that submits a workflow using the 
> examples in the API (scripts/api).
> 
> When I run the WF on data in the LIBRARIES everything works fine.
> But when I choose a HISTORY as my source of data, the WF executes fine, but 
> the history I use is emptied of all the files in there!
> 
> This is very bizarreAny ideas what is going on here?
> I know not a lot of people are using the API, but it is the only way I can 
> run paired end WF on more than a couple of samples...
> 
> Regards,
> 
> Thon de Boer, Ph.D.
> Bioinformatics Guru
> +1-650-799-6839
> thondeb...@me.com
> LinkedIn Profile
> 
> 
> 
> 
> ___
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Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

[Dannon Baker]

I see the bug you're running into.  As a temporary solution, executing 
workflows via the API with 'no_add_to_history' in the payload should work as 
expected.  I'll have a permanent fix out shortly.

-Dannon

On Jul 5, 2012, at 5:12 PM, Thon Deboer wrote:

> Hi,
> 
> I am continueing to struggle with the API
> 
> I have created a workflow execution engine that submits a workflow using the 
> examples in the API (scripts/api).
> 
> When I run the WF on data in the LIBRARIES everything works fine.
> But when I choose a HISTORY as my source of data, the WF executes fine, but 
> the history I use is emptied of all the files in there!
> 
> This is very bizarreAny ideas what is going on here?
> I know not a lot of people are using the API, but it is the only way I can 
> run paired end WF on more than a couple of samples...
> 
> Regards,
> 
> Thon de Boer, Ph.D.
> Bioinformatics Guru
> +1-650-799-6839
> thondeb...@me.com
> LinkedIn Profile
> 
> 
> 
> 
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Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

[Thon Deboer]

Is this conference open for anyone or just (self appointed?) Czars? :)
Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839
thondeb...@me.com
LinkedIn Profile




On Jun 28, 2012, at 2:14 AM, Sebastian Schaaf wrote:

> Also hello to everyone,
> 
> As I browsed through those tabs which are open for weeks I rediscovered the 
> online survey "Interested in Deploying Your Own Local Galaxy?" connected to 
> this thread here. The last response I could find in this context was the one 
> below which was written by Ann.
> To make it short: did anything happen in the meantime, has there been any 
> telephone conference, is there still any interest out there? I filled out the 
> survey and ask myself wether it makes still sense to submit the form. 
> Regarding the fact I can participate in this year's Galaxy Developers 
> Conference (GCC in Chicago) I would be quite happy if some contacts may arise 
> from this thread or the conference or both in a mutual way (which would be 
> somewhat perfect). The heavily discussed topic regarding time zones should 
> not prevent us from going ahead.
> 
> Best regards and thanks in advance,
> 
> Sebastian Schaaf
> (Munich, Germany)
> 
> 
> Ann Black-Ziegelbein schrieb:
>> Hello everyone!
>> 
>> Here is a link to a brief survey about how you are using, or plan to use 
>> Galaxy locally.  If you could take a moment to complete the survey, it will 
>> help steer the teleconferences as we get going (and also alleviate having to 
>> spend time on the call providing the same background info).  The results of 
>> the survey will be made public off of a new wiki site that Galaxy's Dave 
>> Clements is arranging for the group - thanks Dave!
>> 
>> Web Survey: 
>> https://docs.google.com/spreadsheet/viewform?formkey=dGJZcmxEWDQ3aERPNmlBaDl1eHVsQ3c6MQ
>> 
>> Once the teleconference infrastructure details are in place and finalized, I 
>> will send out a web poll to see if we can find a time that works for the 
>> majority.
>> 
>> Thanks,
>> 
>> Ann Black-Ziegelbein
>> 
>> 
>> 
>> On 4/27/2012 2:14 PM, Ryan Golhar wrote:
>>> This is a great idea.
>>> 
>>> On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein 
>>> mailto:annbl...@eng.uiowa.edu>> wrote:
>>> 
>>>Hi everyone -
>>> 
>>>Here at the University of Iowa we are working on deploying Galaxy
>>>locally for campus wide access.  I am interested in forming a
>>>community of other institutions trying to deploy Galaxy locally
>>>and mange/operate it on a broad level.  Is anyone else?   If
>>>there is enough interest, possibly we could have  a community
>>>conference call every other month to have an open discussion on
>>>how we are all deploying galaxy, customizations we are making,
>>>problems we are encountering, bugs, and any add-on operations
>>>management for galaxy being developed, etc.
>>> 
>>>Would love to hear from others operating Galaxy or in process of
>>>standing up a local deployment.
>>> 
>>>Thanks!
>>> 
>>>Ann Black-Ziegelbein
>>>___
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>>>in your mail client.  To manage your subscriptions to this
>>>and other Galaxy lists, please use the interface at:
>>> 
>>>http://lists.bx.psu.edu/
>>> 
>>> 
>> 
>> 
>> 
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> 
>>   http://lists.bx.psu.edu/
> 
> 
> -- 
> Sebastian Schaaf, M.Sc. Bioinformatics
> Chair of Biometry and Bioinformatics
> Department of Medical Information Sciences, Biometry and Epidemiology
> University of Munich
> Marchioninistr. 15, K U1 (postal)
> Marchioninistr. 17, U 006 (office)
> D-81377 Munich (Germany)
> Tel: +49 89 2180-78229
> 
> ___
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[galaxy-dev] History items get REMOVED when using the API to run workflows

[Thon Deboer]

Hi,

I am continueing to struggle with the API

I have created a workflow execution engine that submits a workflow using the 
examples in the API (scripts/api).

When I run the WF on data in the LIBRARIES everything works fine.
But when I choose a HISTORY as my source of data, the WF executes fine, but the 
history I use is emptied of all the files in there!

This is very bizarreAny ideas what is going on here?
I know not a lot of people are using the API, but it is the only way I can run 
paired end WF on more than a couple of samples...

Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839
thondeb...@me.com
LinkedIn Profile




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Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch

[Thon Deboer]

But this only works if you have a single dataset (such as a BAM file) for each 
workflow to run on.
If you have pairs of files (such as paired end FASTQ files, not an uncommon 
workflow nowadays :) ) you need to resort to using the API, since there is no 
support for paired end sequencing in GALAXY in this batch processing from the 
UI (yet?). You can run the Workflow one at a time, but you have to choose the 
FASTQ pairs your self.

I have written a fairly generic execution engine that I can share, that uses a 
config file to describe the files you need from the library in simple key:value 
pairs and that can execute the paired-end sequencing on hundreds of FASTQ 
files...It's a little hacky and requires your FASTQ files to have some 
consistent naming for the forward and reverse reads (_R1.fastq & _R2.fastq) but 
other than that it seems to do the job...

There is however a nasty bug in the API, in that it removes the files from your 
history if you use them in the API (I will post something on that later) but it 
seems to work fine for data in the libraries...

Thon
Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839
thondeb...@me.com
LinkedIn Profile




On Jul 4, 2012, at 12:19 AM, Bernd Jagla wrote:

> Dannon Baker  writes:
> 
>> 
>> Hi Dave,
>> 
>> Yes, galaxy's standard run-workflow dialog has a feature where you can 
>> select 
> multiple datasets as input
>> for a single "Input Dataset" step.  To do this, click the icon referenced by 
> the tooltip in the screenshot
>> below to select multiple files.  All parameters remain static between 
> executions except for the single
>> input dataset that gets modified for each run, and that only one input 
>> dataset 
> can be set to multiple files
>> in this fashion.
>> 
>> -Dannon
> 
> Dannon,
> 
> what if I don't have this icon??? How can I enable this? Where is this 
> documented?
> 
> Thanks,
> 
> Bernd
> 
> 
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Re: [galaxy-dev] Liftover tool installation woes

[Jennifer Jackson]

Great news, very glad this worked. I'll add liftOver to our wiki with 
more specific instructions and add in the bit about explicit paths to 
the .loc file section as well. Should help others going forward.


Thanks for taking the time to report back the solution to the list!

Jen
Galaxy team

On 7/5/12 1:47 AM, Kwon SoonJae wrote:

Hi Jen!

Definitely didn't forget to reset the server everytime I tried. The
problem was solved when I fixed the relative path to the full path..
can't believe I was stuck forever because of such a small miss. Fixed!
and everything working so far =)

Thank you so much,

SJ

On Thu, Jul 5, 2012 at 4:43 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote:

Hello Kwon,

There are no known issues with the liftOver wrapper (tools / extract
/ liftOver_wrapper.py and liftOver_wrapper.xml).

Three more troubleshooting ideas:

1 - This may sound simple, but have you restarted the database since
you updated the .loc files?
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration (final step)

2 - Remove the relative path from the .loc file entries (the "~/"))
and replace with an explicit full path. I personally have not seen
this used before in .loc files. Perhaps others on the list can
comment about whether they have been able to use this successfully
and if any special configuration was necessary.

3- Confirm that the genomes are in your builds list (also covered in
wiki above). Note that UCSC "dbkey" values have special
capitalization rules depending on where they are used. Your example
.loc file has this correct, but I recommend that you also check your
builds list entries against the wiki examples and your actual data.
If you make any changes, be sure to restart before testing.

For example, the liftOver file pair: hg19ToDanRer6.over.chain &
danRer6ToHg19.over.chain
human dbkey = hg19
zebrafish dbkey = danRer6

Please let us know how this works out,

Jen
Galaxy team


On 7/4/12 7:35 PM, Kwon SoonJae wrote:

Hi Jen,

Thanks for looking into this. I have unzipped all the .gz files so
that the directory contains all .chain files. The liftover.loc
file has also been modified to refer to all the .chain files
instead, as such: http://pastebin.com/xSKGvUtG

I still run into the same error if I try to run the tool in
Galaxy, though (hg19ToMm9 mapping currently not available). The
liftover command still works fine through the command line.

I have a feeling the error has to do with the issue with Galaxy's
job runner returning anything written to stderr as an error,
mentioned here:
http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr

Seems like it was an issue back in 2010. Has this been rectified?

Again, thank you for your help,

SJ

On Wed, Jul 4, 2012 at 9:42 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote:

Hello Kwon,

Most of this sounds correct. The only issue is with compressed
files. Galaxy uses uncompressed liftOver data at our site and
this is how we instruct that it be set up (see
galaxy-central/tool-data/liftOver.loc.sample).

Would you be able to run a test to see if uncompressing
resolves the issue? Uncompress one of the over.chain files,
modify the .loc file so that the name also reflects the
uncompressed naming, then try to use the UI version of
liftOver with this uncompressed data. Please let us know how
this works out (cc-ing the list, so that others can learn of
the confirmed dependency).

For now, there is no automated way to enter the .loc data
entries. There is some development activity going on right now
to address data setup (including liftOver), but nothing is
ready yet to be shared. When complete, any new tools will be
announced (loudly - we know that they are highly desired).

Thanks!

Jen
Galaxy team


On 7/3/12 10:21 PM, Kwon SoonJae wrote:

Hi Everyone,

I installed a local instance of galaxy and some tools using
the command line, and for some reason liftover will work in
the command line but won't work in galaxy. Here's what I've
done so far:

- Downloaded liftover standalone executable from the
tool-dependencies page in the Gwiki.

- Changed permissions on liftover executable to make it
usable in the command prompt (terminal, macosx) -> otherwise
I get permission denied.

- Copied executable over to /usr/local/bin likewise to use in
command prompt and in Galaxy.

- Modified liftover.loc to include all the conversion types
and directories of chain.gz files I downloaded to use with
the tool (I believe liftover can make use of both .chain and
.chain.gz files).

After that I tried to run lif

[galaxy-dev] Display with IGV local

[Chebbi Mohamed Amine]

HI Galaxy-team !

I 'am trying  to display  BAM files whith the * local* IGV.
However D*isplay with IGV "local*"  use the already running copy of IGV on
the server machine. So I need evry time to run manually igv by the command
above:
java -Xmx750m -jar igv.jar
Is there any way to do this automatically
I guess that I have to configure bam.xml file to call "java -Xmx750m -jar
igv.jar" command ,  when cliking on D*isplay with IGV local*. ?

Thanks for help
Regards
Amine
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[galaxy-dev] Job output not returned from Cluster

[Sascha Kastens]

Hi all,

 

I have exactly the same problem as described here: 
http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td879580.html

 

All the SGE stuff is administrated in our company and unfortunately they know 
nothing about

Galaxy and so it?s my task to get it running. Everything works fine except the 
problem mentioned

above.

 

I?ve contacted Erick but haven?t received a response yet. If anybody can give 
me some hints where I

can look at to solve the problem or at least what I can tell the admins, I 
would be really grateful.

 

Thanks in advance. If you need further information let me know!

 

Cheers,

Sascha

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[galaxy-dev] Adding the tag in tool xml file

[sshashi]

Hi,

is it possible to add the tag in tool_xml_file ? how can i add new tag
in tool_xml_file ? if anyone is working on this , guide me 

Regards
shashi


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Re: [galaxy-dev] Liftover tool installation woes

[Kwon SoonJae]

Hi Jen!

Definitely didn't forget to reset the server everytime I tried. The problem
was solved when I fixed the relative path to the full path.. can't believe
I was stuck forever because of such a small miss. Fixed! and everything
working so far =)

Thank you so much,

SJ

On Thu, Jul 5, 2012 at 4:43 PM, Jennifer Jackson  wrote:

>  Hello Kwon,
>
> There are no known issues with the liftOver wrapper (tools / extract /
> liftOver_wrapper.py and liftOver_wrapper.xml).
>
> Three more troubleshooting ideas:
>
> 1 - This may sound simple, but have you restarted the database since you
> updated the .loc files?
>   http://wiki.g2.bx.psu.edu/Admin/Data%20Integration (final step)
>
> 2 - Remove the relative path from the .loc file entries (the "~/")) and
> replace with an explicit full path. I personally have not seen this used
> before in .loc files. Perhaps others on the list can comment about whether
> they have been able to use this successfully and if any special
> configuration was necessary.
>
> 3- Confirm that the genomes are in your builds list (also covered in wiki
> above). Note that UCSC "dbkey" values have special capitalization rules
> depending on where they are used. Your example .loc file has this correct,
> but I recommend that you also check your builds list entries against the
> wiki examples and your actual data. If you make any changes, be sure to
> restart before testing.
>
> For example, the liftOver file pair: hg19ToDanRer6.over.chain  &
> danRer6ToHg19.over.chain
> human dbkey = hg19
> zebrafish dbkey = danRer6
>
> Please let us know how this works out,
>
> Jen
> Galaxy team
>
>
> On 7/4/12 7:35 PM, Kwon SoonJae wrote:
>
> Hi Jen,
>
>  Thanks for looking into this. I have unzipped all the .gz files so that
> the directory contains all .chain files. The liftover.loc file has also
> been modified to refer to all the .chain files instead, as such:
> http://pastebin.com/xSKGvUtG
>
>  I still run into the same error if I try to run the tool in Galaxy,
> though (hg19ToMm9 mapping currently not available). The liftover command
> still works fine through the command line.
>
>  I have a feeling the error has to do with the issue with Galaxy's job
> runner returning anything written to stderr as an error, mentioned here:
> http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
>
>  Seems like it was an issue back in 2010. Has this been rectified?
>
>  Again, thank you for your help,
>
>  SJ
>
> On Wed, Jul 4, 2012 at 9:42 PM, Jennifer Jackson  wrote:
>
>>  Hello Kwon,
>>
>> Most of this sounds correct. The only issue is with compressed files.
>> Galaxy uses uncompressed liftOver data at our site and this is how we
>> instruct that it be set up (see
>> galaxy-central/tool-data/liftOver.loc.sample).
>>
>> Would you be able to run a test to see if uncompressing resolves the
>> issue? Uncompress one of the over.chain files, modify the .loc file so that
>> the name also reflects the uncompressed naming, then try to use the UI
>> version of liftOver with this uncompressed data. Please let us know how
>> this works out (cc-ing the list, so that others can learn of the confirmed
>> dependency).
>>
>> For now, there is no automated way to enter the .loc data entries. There
>> is some development activity going on right now to address data setup
>> (including liftOver), but nothing is ready yet to be shared. When complete,
>> any new tools will be announced (loudly - we know that they are highly
>> desired).
>>
>> Thanks!
>>
>> Jen
>> Galaxy team
>>
>>
>> On 7/3/12 10:21 PM, Kwon SoonJae wrote:
>>
>>  Hi Everyone,
>>
>>  I installed a local instance of galaxy and some tools using the command
>> line, and for some reason liftover will work in the command line but won't
>> work in galaxy. Here's what I've done so far:
>>
>>  - Downloaded liftover standalone executable from the tool-dependencies
>> page in the Gwiki.
>>
>>  - Changed permissions on liftover executable to make it usable in the
>> command prompt (terminal, macosx) -> otherwise I get permission denied.
>>
>>  - Copied executable over to /usr/local/bin likewise to use in command
>> prompt and in Galaxy.
>>
>>  - Modified liftover.loc to include all the conversion types and
>> directories of chain.gz files I downloaded to use with the tool (I believe
>> liftover can make use of both .chain and .chain.gz files).
>>
>>  After that I tried to run liftover in Galaxy and it didn't work, giving
>> me some error that said hg19ToMm9 mapping is currently not available. It
>> seems to work fine using the command line though.
>>
>>  Since my goal is to setup galaxy locally, I really want to get this
>> working correctly. Can anyone guide me through what's gone wrong?
>> Also, there must be a better way of installing all these tools than
>> manually downloading every single one and using the command line, surely? I
>> had to type out the format of liftover.loc file manually for around 130
>> chain files... I'm convinced there has to be a better way.

Re: [galaxy-dev] Liftover tool installation woes

[Jennifer Jackson]

Hello Kwon,

There are no known issues with the liftOver wrapper (tools / extract / 
liftOver_wrapper.py and liftOver_wrapper.xml).


Three more troubleshooting ideas:

1 - This may sound simple, but have you restarted the database since you 
updated the .loc files?

  http://wiki.g2.bx.psu.edu/Admin/Data%20Integration (final step)

2 - Remove the relative path from the .loc file entries (the "~/")) and 
replace with an explicit full path. I personally have not seen this used 
before in .loc files. Perhaps others on the list can comment about 
whether they have been able to use this successfully and if any special 
configuration was necessary.


3- Confirm that the genomes are in your builds list (also covered in 
wiki above). Note that UCSC "dbkey" values have special capitalization 
rules depending on where they are used. Your example .loc file has this 
correct, but I recommend that you also check your builds list entries 
against the wiki examples and your actual data. If you make any changes, 
be sure to restart before testing.


For example, the liftOver file pair: hg19ToDanRer6.over.chain  &  
danRer6ToHg19.over.chain

human dbkey = hg19
zebrafish dbkey = danRer6

Please let us know how this works out,

Jen
Galaxy team

On 7/4/12 7:35 PM, Kwon SoonJae wrote:

Hi Jen,

Thanks for looking into this. I have unzipped all the .gz files so 
that the directory contains all .chain files. The liftover.loc file 
has also been modified to refer to all the .chain files instead, as 
such: http://pastebin.com/xSKGvUtG


I still run into the same error if I try to run the tool in Galaxy, 
though (hg19ToMm9 mapping currently not available). The liftover 
command still works fine through the command line.


I have a feeling the error has to do with the issue with Galaxy's job 
runner returning anything written to stderr as an error, mentioned 
here: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr


Seems like it was an issue back in 2010. Has this been rectified?

Again, thank you for your help,

SJ

On Wed, Jul 4, 2012 at 9:42 PM, Jennifer Jackson > wrote:


Hello Kwon,

Most of this sounds correct. The only issue is with compressed
files. Galaxy uses uncompressed liftOver data at our site and this
is how we instruct that it be set up (see
galaxy-central/tool-data/liftOver.loc.sample).

Would you be able to run a test to see if uncompressing resolves
the issue? Uncompress one of the over.chain files, modify the .loc
file so that the name also reflects the uncompressed naming, then
try to use the UI version of liftOver with this uncompressed data.
Please let us know how this works out (cc-ing the list, so that
others can learn of the confirmed dependency).

For now, there is no automated way to enter the .loc data entries.
There is some development activity going on right now to address
data setup (including liftOver), but nothing is ready yet to be
shared. When complete, any new tools will be announced (loudly -
we know that they are highly desired).

Thanks!

Jen
Galaxy team


On 7/3/12 10:21 PM, Kwon SoonJae wrote:

Hi Everyone,

I installed a local instance of galaxy and some tools using the
command line, and for some reason liftover will work in the
command line but won't work in galaxy. Here's what I've done so far:

- Downloaded liftover standalone executable from the
tool-dependencies page in the Gwiki.

- Changed permissions on liftover executable to make it usable in
the command prompt (terminal, macosx) -> otherwise I get
permission denied.

- Copied executable over to /usr/local/bin likewise to use in
command prompt and in Galaxy.

- Modified liftover.loc to include all the conversion types and
directories of chain.gz files I downloaded to use with the tool
(I believe liftover can make use of both .chain and .chain.gz files).

After that I tried to run liftover in Galaxy and it didn't work,
giving me some error that said hg19ToMm9 mapping is currently not
available. It seems to work fine using the command line though.

Since my goal is to setup galaxy locally, I really want to get
this working correctly. Can anyone guide me through what's gone
wrong?
Also, there must be a better way of installing all these tools
than manually downloading every single one and using the command
line, surely? I had to type out the format of liftover.loc file
manually for around 130 chain files... I'm convinced there has to
be a better way.

Thanks in advance,

SJ


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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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-- 
Jennifer Jackson

http://galaxyproject.or