from:"Previti"

[galaxy-dev] Re: Bismark - Bug in Bismark Pretty Report ?

2019-07-15 Thread Previti

Dear Björn,

This works now...but I don't know why...
Maybe a combination of a Galaxy update and correctly whitelisting the
tool for displaying html output

Thanks for getting back to me!

Christopher


On 7/13/19 1:45 PM, Björn Grüning wrote:
> Uha, this looks like a upstream bug, not sure how this can be Galaxy
> related.
>
> Is this still a problem?
>
> Cheers,
> Bjoern
>
> Am 08.03.19 um 09:23 schrieb Previti:
>> Dear Galaxy Community,
>>
>> I just recently started testing the Bismark methylation tools,
>> everything works fine until I try to make a "pretty report".
>> Some information is not included in the report, instead you see
>> placeholders
>> I attached the output I  get and shown below are the job parameters.
>> Does anybody know where to fix this?
>>
>> Best regards,
>> Christopher
>>
>>
>>     Bismark Pretty Report
>>
>>
>>   Dataset Information
>>
>> Number: 198
>> Name: Bismark Pretty Report on data 190, data 189, and others:
>> Download pretty html report
>> Created: Thu 07 Mar 2019 03:24:40 PM (UTC)
>> Filesize: 2.7 MB
>> Dbkey: ?
>> Format: html
>>
>>
>>   Job Information
>>
>> Galaxy Tool ID:
>> toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_pretty_report/0.20.0
>> Galaxy Tool Version: 0.20.0
>> Tool Version:
>> Tool Standard Output: stdout
>> <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stdout>
>> Tool Standard Error: stderr
>> <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stderr>
>> Tool Exit Code: 0
>> History Content API ID: 971c2f882eb14ac3 (41433)
>> Job API ID: 58816697357e736f (22051)
>> History API ID: 5fccce9c1b3793da (807)
>> UUID: 45bedd12-6ce5-4d63-a1e2-e05883b0c356
>> Full Path: /opt/galaxy/galaxy/database/files/038/dataset_38737.dat
>>
>>
>>   Tool Parameters
>>
>> Input Parameter Value Note for rerun
>> Submit a Bismark mapping report 191: Bismark Meth. Extractor on
>> data 60 and data 133: Genome-wide methylation report.
>> <http://dkfzgalaxy/datasets/c53067deacfc4f28/show_params>
>> additional_reports
>> Submit the corresponding Bismark deduplication report 197:
>> Bismark Deduplicate on data 133: deduplication report
>> <http://dkfzgalaxy/datasets/622377f5e70addd2/show_params>
>> Submit the corresponding Bismark splitting report 189: Bismark
>> Meth. Extractor on data 60 and data 133: Splitting Report
>> <http://dkfzgalaxy/datasets/aa40ffd063a4645f/show_params>
>> Submit the corresponding Bismark M-bias report 190: Bismark Meth.
>> Extractor on data 60 and data 133: Mbias Report
>> <http://dkfzgalaxy/datasets/47db6b20871008b9/show_params>
>> Submit the corresponding Bismark nucleotide report
>> 
>> Create a separate logfile, otherwise logs are added to the dataset
>> info. False
>>
>>
>>   Inheritance Chain
>>
>> Bismark Pretty Report on data 190, data 189, and others: Download
>> pretty html report
>>
>>
>>   Command Line
>>
>> python
>> '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/bismark/7bffcb6fc81d/bismark/bismark2report_wrapper.py'
>>  
>> --alignment_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38715.dat' 
>> --dedup_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38736.dat'
>> --splitting_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38713.dat'
>> --mbias_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38714.dat' 
>> --output_html_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38737.dat'
>>
>>
>>   Job Metrics
>>
>>
>>     core
>>
>> Cores Allocated 8
>> Job End Time 2019-03-07 16:49:58
>> Job Runtime (Wall Clock) 25 minutes
>> Job Start Time 2019-03-07 16:24:43
>> Memory Allocated (MB) 51
>>
>>
>>   Job Dependencies
>>
>> Dependency Dependency Type Version
>> bismark conda 0.20.0
>>
>>
>>
>> -- 
>> *Dr. Christopher Previti*
>> Genomics and Proteomics Core Facility
>> High Throughput Sequencing (W190)
>> Bioinformatician
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 580
>> 69120 Heidelberg
>> Germany
>> Room: B2.102 (INF580/TP3)
>> Phone:

[galaxy-dev] Re: Error during tool installation: "inotify instance limit reached"

2019-07-10 Thread Previti

Thank you very much!

We have 19.01 running and the parameter that I had to put to "false" was
"watch_tools"

All the best,
Christopher


On 7/10/19 12:00 PM, Marius van den Beek wrote:
> Hi Christopher,
>
> you might want to turn off `watch_tools` if you are using it,
> this is only needed when using the pretty-much undocumented
> feature where you dump tools into a directory without registering them
> in any tool_conf.xml file. All other tool reloading happens by another
> means.
>
> Similarly, if you're using 19.05 and you don't manipulate the tool
> data table
> entries manually you can disable `watch_tool_data_dir`.
>
> Finally this is usually a sign of allocating too many processes and
> threads for your webservers/handlers/mules,
> as each one starts their own watchdog. A common misconception is that
> this makes Galaxy run faster.
> but it actually just increases the amount of concurrent requests
> Galaxy can handle.
>
> Best,
> Marius
>
> On Wed, 10 Jul 2019 at 11:43, Previti
>  <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>
> Dear all,
>
> I've been getting this error for a few days now, it basically prevents
> anything from being installed on the first go.
> Individual tools can be installed, but even then I have to try
> multiple
> times.
>
> Any ideas how to fix this?
>
> Cheers,
> Christopher
>
> The details from galaxy.log are (installing an older VCFtools
> package):
>
> 172.22.24.119 - - [10/Jul/2019:10:44:32 +0200] "POST
> /admin_toolshed/prepare_for_install HTTP/1.1" 200 -
> 
> "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install?change
> 
> set_revisions=34a6b690e4b5_ids=2ba42187f2588c4b_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F
> 
> <http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install?changeset_revisions=34a6b690e4b5_ids=2ba42187f2588c4b_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F>"
> "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101
> Firefox/67.0"
> galaxy.tools.toolbox.base DEBUG 2019-07-10 10:44:55,592 Appending to
> tool panel section: NGS:VCFtools
> 172.22.24.119 - - [10/Jul/2019:10:44:58 +0200] "POST
> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 -
> "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare
> _for_install" "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0)
> Gecko/20100101 Firefox/67.0"
> 172.22.24.119 - - [10/Jul/2019:10:45:01 +0200] "POST
> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 -
> "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare
> _for_install" "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0)
> Gecko/20100101 Firefox/67.0"
> 172.22.24.119 - - [10/Jul/2019:10:44:55 +0200] "POST
> /admin_toolshed/install_repositories HTTP/1.1" 500 -
> 
> "http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install;
> "Moz
> illa/5.0 (X11; Fedora; Linux x86_64; rv:67.0) Gecko/20100101
> Firefox/67.0"
> *Error - : inotify instance limit reached*
> URL:
> 
> http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/install_repositories
> File
> '/opt/galaxy/galaxy/lib/galaxy/web/framework/middleware/error.py',
> line 154 in __call__
>   app_iter = self.application(environ, sr_checker)
> File
> '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py',
> line 85 in __call__
>   return self.application(environ, start_response)
> File
> 
> '/opt/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py',
> line 640 in __call__
>   return self.application(environ, start_response)
> File '/opt/galaxy/galaxy/lib/galaxy/web/framework/base.py', line
> 143 in
> __call__
>   return self.handle_request(environ, start_response)
> File '/opt/galaxy/galaxy/lib/galaxy/web/framework/base.py', line
> 222 in
> handle_request
>   body = method(trans, **kwargs)
> File '/opt/galaxy/galaxy/lib/galaxy/web/framework/decorators.py', line
> 101 in decorator
>   return func(self, trans, *args, **kwargs)
> File
> 
> '/opt/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> line 575 in install_repositories
>   reinstalling=reinstalling,
> File
> '/opt/galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py',
> line 846 in install_r

[galaxy-dev] Error during tool installation: "inotify instance limit reached"

2019-07-10 Thread Previti

*
**  raise OSError("inotify instance limit reached")**
**OSError: inotify instance limit reached**
*
CGI Variables
-
  CONTENT_LENGTH: '12169'
  CONTENT_TYPE: 'application/x-www-form-urlencoded; charset=UTF-8'
  HTTP_ACCEPT: 'text/html, */*; q=0.01'
  HTTP_ACCEPT_ENCODING: 'gzip,deflate'
  HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
  HTTP_CONNECTION: 'Keep-Alive'
  HTTP_COOKIE:
'galaxysession=c6ca0ddb55be603a9d01bef828912a83dd6a820b8a47ad278d223920b71ba8b43726aaf1140b008e'
  HTTP_HOST: 'dkfzgalaxy.inet.dkfz-heidelberg.de'
  HTTP_REFERER:
'http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/prepare_for_install'
  HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:67.0)
Gecko/20100101 Firefox/67.0'
  HTTP_X_FORWARDED_FOR: '172.22.24.119'
  HTTP_X_FORWARDED_HOST: 'dkfzgalaxy.inet.dkfz-heidelberg.de'
  HTTP_X_FORWARDED_SERVER: 'fe80::216:3eff:fe80:c02b'
  HTTP_X_REQUESTED_WITH: 'XMLHttpRequest'
  ORGINAL_HTTP_HOST: 'localhost:8080'
  ORGINAL_REMOTE_ADDR: '127.0.0.1'
  PATH_INFO: '/admin_toolshed/install_repositories'
  REMOTE_ADDR: '172.22.24.119'
  REQUEST_METHOD: 'POST'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--
  application: 
  controller_action_key: u'web.admin_toolshed.install_repositories'
  is_api_request: False
  paste.cookies: (,
'galaxysession=c6ca0ddb55be603a9d01bef828912a83dd6a820b8a47ad278d223920b71ba8b43726aaf1140b008e')
  paste.expected_exceptions: []
  paste.httpexceptions: 
  paste.httpserver.proxy.host: 'dummy'
  paste.httpserver.proxy.scheme: 'http'
  paste.httpserver.thread_pool: 
  paste.recursive.forward: 
  paste.recursive.include: 
  paste.recursive.include_app_iter: 
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: 'fd8cc98ea2ee11e9a89100163e80c02b'
  webob._body_file: (<_io.BufferedReader>, )
  webob._parsed_post_vars: (MultiDict([('tool_shed_repository_ids',
u"[u'ac218635d795e337', u'e3e09dfaa8fad8c8', u'1efe9eb0bff40152',
u'358d8704ef89cb6b', u'cbc5119f47881258']"), ('encoded_kwd',
u'59b03a7799b953da9827424b9cef2236c5b9f461:7b22737461747573223a2022646f6e65222c20226861735f7265706f7369746f72795f646570656e64656e63696573223a2066616c73652c2022696e636c756465735f746f6f6c735f666f725f646973706c61795f696e5f746f6f6c5f70616e656c223a20747275652c2022746f6f6c5f736865645f7265706f7369746f72795f696473223a205b226163323138363335643739356537222c202265336530396466616138666164386338222c2022316566653965623062343031353c20223335386438373034656638396362366c202263626335313139663437383831323538225d2c2022736865645f746f6f6c5f636f6e66223a20222e2f636f6e6669672f736865645f746f6f6c5f636f6e662e786d6c222c2022696e7374616c6c5f7265706f7369746f72795f646570656e64656e63696573223a20747275652c2022746f6f6c5f70617468223a20222f6f70742f67616c6178792f736865645f746f6f6c73222c20227265706f5f696e666f5f6469637473223a2...
0x7f9f35cdfed0>)
  webob._parsed_query_vars: (GET([]), '')
  webob.is_body_seekable: True
  wsgi process: 'Multithreaded'
  wsgi.input_terminated: True




-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
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Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
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[galaxy-dev] Re: Serious issues with picard-tools after upgrade to Galaxy version 19.01

2019-03-20 Thread Previti

Update:

The bam file is usable as long as the correct sorting order is
specified. The new datatype "qname_sorted.bam" is not automatically set
if the sorting order is
by "queryname" (Read identifier).
As long as the bam is not mapped I get:

/Could not display BAM file, error was:file has no sequences defined
(mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False//
/
When I try to visualize it.

I hope I helped somebody with these infos.

Christopher

On 3/15/19 4:43 PM, Previti wrote:
> Dear all,
>
> I'm having serious issues with picard tools (latest Galaxy version
> 2.18.2.1 by devteam) after upgrading our galaxy to version 19.01
> I've been running fastqtoSam on paired-end data:
>
> _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx200g -Xms256m'} && export _JAVA_OPTIONS 
> &&  
> picard FastqToSam  
> FASTQ="/opt/galaxy/galaxy/database/files/039/dataset_39081.dat" 
> FASTQ2="/opt/galaxy/galaxy/database/files/039/dataset_39082.dat"  
> QUALITY_FORMAT="Standard" 
> OUTPUT="/opt/galaxy/galaxy/database/files/039/dataset_39441.dat" 
> READ_GROUP_NAME="A" SAMPLE_NAME="sample-a" 
> MIN_Q="0" MAX_Q="93" 
> STRIP_UNPAIRED_MATE_NUMBER="false" 
> ALLOW_AND_IGNORE_EMPTY_LINES="false"  
> SORT_ORDER=coordinate 
> VALIDATION_STRINGENCY="LENIENT" 
> QUIET=true VERBOSITY=ERROR  `if [ -n "$TMPDIR" ] ; then echo 
> 'TMP_DIR=$TMPDIR' ; else if [ -n "$TEMP" ] ; then echo 'TMP_DIR=$TEMP' ; fi ; 
> fi`
>
> But the bam file I get is not readable and I also get following message:
>
> Picked up _JAVA_OPTIONS: -Xmx200g -Xms256m
> 14:16:29.629 INFO  NativeLibraryLoader - Loading libgkl_compression.so 
> from 
> jar:file:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__picard@2.18.2/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
>
> does anybody know what's going on?
> The output "bam" file is the correct size (>20GB) but not readable...
>
> Thanks and best regards,
> Christopher Previti
>
>
>  
> *Dr. Christopher Previti*
> Genomics and Proteomics Core Facility
> High Throughput Sequencing (W190)
> Bioinformatician
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 580
> 69120 Heidelberg
> Germany
> Room: B2.102 (INF580/TP3)
> Phone: +49 6221 42-4661
>
> christopher.prev...@dkfz.de <http://www.dkfz.de/>
> www.dkfz.de <http://www.dkfz.de/>
>
> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> VAT-ID No.: DE143293537
>
> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
> Personen bestimmt, an die sie adressiert ist.
> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
> Informationen enthalten. Sollten Sie nicht
> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
> Absender und löschen Sie die Mitteilung.
> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
> untersagt.
>
>
> ___
> 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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>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
Please keep all replies on the list by using "reply all"
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[galaxy-dev] Serious issues with picard-tools after upgrade to Galaxy version 19.01

2019-03-15 Thread Previti

Dear all,

I'm having serious issues with picard tools (latest Galaxy version
2.18.2.1 by devteam) after upgrading our galaxy to version 19.01
I've been running fastqtoSam on paired-end data:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx200g -Xms256m'} && export _JAVA_OPTIONS &&  
picard FastqToSam  
FASTQ="/opt/galaxy/galaxy/database/files/039/dataset_39081.dat" 
FASTQ2="/opt/galaxy/galaxy/database/files/039/dataset_39082.dat"  
QUALITY_FORMAT="Standard" 
OUTPUT="/opt/galaxy/galaxy/database/files/039/dataset_39441.dat" 
READ_GROUP_NAME="A" SAMPLE_NAME="sample-a" 
MIN_Q="0" MAX_Q="93" 
STRIP_UNPAIRED_MATE_NUMBER="false" 
ALLOW_AND_IGNORE_EMPTY_LINES="false"  
SORT_ORDER=coordinate 
VALIDATION_STRINGENCY="LENIENT" 
QUIET=true VERBOSITY=ERROR  `if [ -n "$TMPDIR" ] ; then echo 'TMP_DIR=$TMPDIR' 
; else if [ -n "$TEMP" ] ; then echo 'TMP_DIR=$TEMP' ; fi ; fi`

But the bam file I get is not readable and I also get following message:

Picked up _JAVA_OPTIONS: -Xmx200g -Xms256m
14:16:29.629 INFO  NativeLibraryLoader - Loading libgkl_compression.so 
from 
jar:file:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__picard@2.18.2/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

does anybody know what's going on?
The output "bam" file is the correct size (>20GB) but not readable...

Thanks and best regards,
Christopher Previti


 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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[galaxy-dev] Bugfix for CollectRNAmetrics (Picardtools)

2019-01-29 Thread Previti

Dear all,

I just fixed a bug that prevented CollectRNAmetrics (a Picard-Tool,
galaxy version 2.7.1) from working with  GTF annotation files:

The pre-processing step that converts gtf  to the genepred format needs
two extra parameters (marked red):

gtfToGenePred -genePredExt -geneNameAsName2 'test.gtf' refFlat.tab.raw


The format of my GTF is:


Seqname Source  Feature Start   End Score   Strand  Frame   
Attributes
3R  FlyBase gene722370  722621  .   -   .   gene_id 
"FBgn0085804";
gene_name "CR41571"; gene_source "FlyBase"; gene_biotype "pseudogene";



I'm assuming this is the "standard" GTF format (according to ensembl)

How's the best way to make this type of thing known...?

Cheers,
Christopher

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

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Re: [galaxy-dev] Input paired dataset collection in workflow

2019-01-24 Thread Christopher Previti


I got it, sorry to bother you.
One can actually specify the type of collection...and set it to list of 
dataset pairs.

Best regards,
Christopher


Am 24.01.19 um 10:19 schrieb Christopher Previti:


Dear Galaxy Community,

Is there a way to input a paired dataset collection into a workflow?

I would like to build a workflow using cutadapt with a paired dataset 
collection but...I'm missing something.


I have seen workflows (at usegalaxy.eu for example: 
1_CLIPseq-Explorer_demulti_PEAKachu_iCLIP_hg19) where this is possible.


But how is this done practically?

Thanks and best regards,

Christopher


Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die 
Personen bestimmt, an die sie adressiert ist.
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Absender und löschen Sie die Mitteilung.
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[galaxy-dev] Input paired dataset collection in workflow

2019-01-24 Thread Christopher Previti


Dear Galaxy Community,

Is there a way to input a paired dataset collection into a workflow?

I would like to build a workflow using cutadapt with a paired dataset 
collection but...I'm missing something.


I have seen workflows (at usegalaxy.eu for example: 
1_CLIPseq-Explorer_demulti_PEAKachu_iCLIP_hg19) where this is possible.


But how is this done practically?

Thanks and best regards,

Christopher


Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.prev...@dkfz.de 
www.dkfz.de 

logo 

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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Personen bestimmt, an die sie adressiert ist.
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Re: [galaxy-dev] Fastq.gz datatype not recognized on import to data library

2018-12-03 Thread Previti

Ok, I submitted it, hope somebody can help with this.

Cheers,
Christoper

On 12/3/18 3:20 PM, Nicola Soranzo wrote:
> Hi Christopher,
> can you please submit an issue for this at
> https://github.com/galaxyproject/galaxy/issues/ with the relevant logs
> and/or tracebacks?
>
> Cheers,
> Nicola
>
> On 03/12/2018 13:33, Previti wrote:
>> Dear all,
>>
>> In my ongoing saga concerning our data libraries, I came across
>> another issue after our update from 17.09 to 18.05.
>> When trying to import fastq.gz files into a data library (linking the
>> files from a user directory), the format is not recognized
>> automatically.
>>
>> I specifically have to set the data type to fastq.gz in order for it
>> to work at all and even then it sometimes ends up throwing an error
>> (state = error).
>>
>> Is there anything in particular I need to change to make this work
>> reliably?
>>
>> Cheers,
>>
>> Christopher
>>
>>
>>
>> -- 
>> *Dr. Christopher Previti*
>> Genomics and Proteomics Core Facility
>> High Throughput Sequencing (W190)
>> Bioinformatician
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 580
>> 69120 Heidelberg
>> Germany
>> Room: B2.102 (INF580/TP3)
>> Phone: +49 6221 42-4661
>>
>> christopher.prev...@dkfz.de <http://www.dkfz.de/>
>> www.dkfz.de <http://www.dkfz.de/>
>>
>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
>> VAT-ID No.: DE143293537
>>
>> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
>> Personen bestimmt, an die sie adressiert ist.
>> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
>> Informationen enthalten. Sollten Sie nicht
>> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
>> Absender und löschen Sie die Mitteilung.
>> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht
>> ist untersagt.
>>
>>
>>
>> ___
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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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>>
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>>   http://galaxyproject.org/search/
>
>
> ___
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-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


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[galaxy-dev] Fastq.gz datatype not recognized on import to data library

2018-12-03 Thread Previti

Dear all,

In my ongoing saga concerning our data libraries, I came across another
issue after our update from 17.09 to 18.05.
When trying to import fastq.gz files into a data library (linking the
files from a user directory), the format is not recognized automatically.

I specifically have to set the data type to fastq.gz in order for it to
work at all and even then it sometimes ends up throwing an error (state
= error).

Is there anything in particular I need to change to make this work reliably?

Cheers,

Christopher



-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
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Re: [galaxy-dev] Using soft-links to NFS-shares as user directories

2018-11-30 Thread Previti

Dear all,
I got it to work again.
I just added:

user_library_import_symlink_whitelist = "/symlink_target_folder"/

to the galaxy.ini (we'll switch to the .yml next update).
It got recognized and the symlinks can be used again.

Best regards,
Christopher

On 11/28/18 9:25 AM, Previti wrote:
> Thanks for the infos, I guess we will just have to check everything
> again.
> I wonder, did anything change from 17.09 to 18.05 that would affect
> the way the system resolves the email-addresses?
>
> We'll let everybody know if we have a solution/cause for the problem.
>
> Cheers and thanks again,
> Christopher
>
> On 11/27/18 11:00 PM, Youssef GHORBAL wrote:
>> Hello,
>>
>> As per
>> this 
>> https://github.com/galaxyproject/galaxy/blob/9a6fddcdca7042e5e453bdd235ed8c5b3266fb7d/lib/galaxy/webapps/galaxy/api/remote_files.py#L54
>> The message you are seeing "You do not have any files in your user
>> directory. Use FTP to upload there" has nothing to do
>> with user_library_import_symlink_whitelist
>> The symlink control (involving user_library_import_symlink_whitelist)
>> is done a little bit later in the code.
>>
>> The test code is rather straightforward it does an os.path.exists on
>> the path contact of the user_library_import_dir setting and the
>> user's email address.
>>
>> Option 1: Galaxy is not resolving the correct email address for your
>> account, I don't see why this may change after upgrade. But it's
>> worth double checking (especially the case)
>> Option 2: There is an issue with permissions on the symlink target.
>> I've checked python will return false on os.path.exists if the
>> symlink targets a directory not accessible by the user.
>> For me you need to double check the permissions on your server. Maybe
>> with a shell access as the gal...@ad.dkfz-heidelberg.de
>> <mailto:gal...@ad.dkfz-heidelberg.de> user, you can try access one of
>> the symlinks and see how it goes. You may also check that the Galaxy
>> service is actually running under the intended identity
>> (gal...@ad.dkfz-heidelberg.de <mailto:gal...@ad.dkfz-heidelberg.de>)
>>
>> Youssef Ghorbal
>> IIS / DSI
>> Institut Pasteur
>> -
>>> On 27 Nov 2018, at 11:43, Previti
>>> >> <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>>>
>>> Dear Youssef,
>>> Thanks for answering, the target permissions have not changed and
>>> are defined via NFS4 ACLs:
>>>
>>> A::OWNER@:rwaDxtTnNcCy
>>> A::GROUP@:rwaDxtTnNcy
>>> *A:fdi:gal...@ad.dkfz-heidelberg.de:rwaDxtTnNcy*
>>> A:fdig:w190-galaxy-adm...@ad.dkfz-heidelberg.de:rwaDxtTnNcy
>>>
>>> In this case the galaxy user (i.e. the user starting the process)
>>> has full access to the share.
>>> In our instance the "user directories" are just symbolic links to
>>> the target folders mention above.
>>> When I try to import data from a user directory/NFS4 share into a
>>> data library we get the following error: 
>>>
>>> "You do not habe any files in your user directory. Use FTP to upload
>>> there." (I attached a screenshot)
>>>
>>> We still use galaxy.ini to configure our instance, in the galaxy.yml
>>> I find the following parameter:
>>>
>>> # For security reasons, users may not import any files that actually
>>>   # lie outside of their `user_library_import_dir` (e.g. using symbolic
>>>   # links). A list of directories can be allowed by setting the
>>>   # following option (the list is comma-separated). Be aware that *any*
>>>   # user with library import permissions can import from anywhere in
>>>   # these directories (assuming they are able to create symlinks to
>>>   # them).
>>>   #user_library_import_symlink_whitelist: null
>>>
>>> Would implementing this solve my issue?
>>>
>>> Cheers,
>>> Christopher
>>>
>>>
>>>
>>> On 11/26/18 4:36 PM, Youssef GHORBAL wrote:
>>>> Hello,
>>>>
>>>> What do you mean exactly "doesn't work anymore" ? Do current links
>>>> no longer appear in data-library ? Do new soft-links can no longer
>>>> be made available into data-library ? Do you have any error messages ?
>>>> By the way the symlink permissions are not valuable, you need to
>>>> check the target permissions (/galaxy-clients/w190_galaxy/ for
>>>> instance)
>>>>
>>>> Youssef

Re: [galaxy-dev] Using soft-links to NFS-shares as user directories

2018-11-28 Thread Previti

Thanks for the infos, I guess we will just have to check everything again.
I wonder, did anything change from 17.09 to 18.05 that would affect the
way the system resolves the email-addresses?

We'll let everybody know if we have a solution/cause for the problem.

Cheers and thanks again,
Christopher

On 11/27/18 11:00 PM, Youssef GHORBAL wrote:
> Hello,
>
> As per
> this 
> https://github.com/galaxyproject/galaxy/blob/9a6fddcdca7042e5e453bdd235ed8c5b3266fb7d/lib/galaxy/webapps/galaxy/api/remote_files.py#L54
> The message you are seeing "You do not have any files in your user
> directory. Use FTP to upload there" has nothing to do
> with user_library_import_symlink_whitelist
> The symlink control (involving user_library_import_symlink_whitelist)
> is done a little bit later in the code.
>
> The test code is rather straightforward it does an os.path.exists on
> the path contact of the user_library_import_dir setting and the user's
> email address.
>
> Option 1: Galaxy is not resolving the correct email address for your
> account, I don't see why this may change after upgrade. But it's worth
> double checking (especially the case)
> Option 2: There is an issue with permissions on the symlink target.
> I've checked python will return false on os.path.exists if the symlink
> targets a directory not accessible by the user.
> For me you need to double check the permissions on your server. Maybe
> with a shell access as the gal...@ad.dkfz-heidelberg.de
> <mailto:gal...@ad.dkfz-heidelberg.de> user, you can try access one of
> the symlinks and see how it goes. You may also check that the Galaxy
> service is actually running under the intended identity
> (gal...@ad.dkfz-heidelberg.de <mailto:gal...@ad.dkfz-heidelberg.de>)
>
> Youssef Ghorbal
> IIS / DSI
> Institut Pasteur
> -
>> On 27 Nov 2018, at 11:43, Previti
>> > <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>>
>> Dear Youssef,
>> Thanks for answering, the target permissions have not changed and are
>> defined via NFS4 ACLs:
>>
>> A::OWNER@:rwaDxtTnNcCy
>> A::GROUP@:rwaDxtTnNcy
>> *A:fdi:gal...@ad.dkfz-heidelberg.de:rwaDxtTnNcy*
>> A:fdig:w190-galaxy-adm...@ad.dkfz-heidelberg.de:rwaDxtTnNcy
>>
>> In this case the galaxy user (i.e. the user starting the process) has
>> full access to the share.
>> In our instance the "user directories" are just symbolic links to the
>> target folders mention above.
>> When I try to import data from a user directory/NFS4 share into a
>> data library we get the following error: 
>>
>> "You do not habe any files in your user directory. Use FTP to upload
>> there." (I attached a screenshot)
>>
>> We still use galaxy.ini to configure our instance, in the galaxy.yml
>> I find the following parameter:
>>
>> # For security reasons, users may not import any files that actually
>>   # lie outside of their `user_library_import_dir` (e.g. using symbolic
>>   # links). A list of directories can be allowed by setting the
>>   # following option (the list is comma-separated). Be aware that *any*
>>   # user with library import permissions can import from anywhere in
>>   # these directories (assuming they are able to create symlinks to
>>   # them).
>>   #user_library_import_symlink_whitelist: null
>>
>> Would implementing this solve my issue?
>>
>> Cheers,
>> Christopher
>>
>>
>>
>> On 11/26/18 4:36 PM, Youssef GHORBAL wrote:
>>> Hello,
>>>
>>> What do you mean exactly "doesn't work anymore" ? Do current links
>>> no longer appear in data-library ? Do new soft-links can no longer
>>> be made available into data-library ? Do you have any error messages ?
>>> By the way the symlink permissions are not valuable, you need to
>>> check the target permissions (/galaxy-clients/w190_galaxy/ for instance)
>>>
>>> Youssef Ghorbal
>>> IIS / DSI
>>> Institut Pasteur
>>> ---
>>>> On 26 Nov 2018, at 15:23, Previti
>>>> >>> <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> We implemented a system using soft-links to link user-directories
>>>> to NFS shares in order to import/link datasets that are larger than
>>>> 2GB (through links to data-libraries) and provide our users with
>>>> longer term storage space for their analyses.
>>>> This worked fine for Galaxy version 17.09...and stopped working for
>>&

[galaxy-dev] Using soft-links to NFS-shares as user directories

2018-11-26 Thread Previti

Dear all,

We implemented a system using soft-links to link user-directories to NFS
shares in order to import/link datasets that are larger than 2GB
(through links to data-libraries) and provide our users with longer term
storage space for their analyses.
This worked fine for Galaxy version 17.09...and stopped working for
Version 18.05.

An example can be seen here in the folder (the path to this folder will
vary between installations): /opt/galaxy/galaxy/database/files

lrwxrwxrwx   1 galaxy  W190-htseq-bioinf  28 Sep 11 12:37
christopher.prev...@dkfz-heidelberg.de -> /galaxy-clients/w190_galaxy/

Setting the proper rights allows users to link files from the nfs
data-share make available under /galaxy-clients (in this case the share 
is called "w190_galaxy")
directly into a data-library (with the approriate rights).

Would anybody have an idea why this doesn't work anymore in v18.05?
Is it a galaxy.ini configuration issue?

Thanks for any advise you could provide!

Christopher




-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


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[galaxy-dev] Bug in data manager for the STAR aligner indices

2018-11-12 Thread Previti

Dear all,

I've been wanting to point this out for a while, but the latest update
to the STAR data manager didn't fix it either (or maybe I messed up again).
The .loc file indicating which genomes have been installed/indices have
been made for STAR uses the last column to indicate if there
is a gene model/annotation that it should use (0 - for no, 1 - for yes).
This seems to be empty...there is a tab at the end of the row,  but no
number.
It works if you manually but in 1 or 0, but not that's not very convenient.

Please let me know if I'm missing something...

Cheers,
Christopher

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


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Re: [galaxy-dev] Error after creating dataset list of bam files in v18.05

2018-10-23 Thread Previti

Ok thanks!

On 10/23/2018 11:14 AM, Marius van den Beek wrote:
> Dear Christopher,
>
> You need to copy the shipped datatypes_conf.xml.sample to the
> appropriate location(s) for your installation.
>
> Best,
> Marius
>
>
> On Tue, Oct 23, 2018, 11:08 AM Previti
>  <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>
> Dear all,
>
> We're in the process of testing version 18.05 before updating our
> production server.
> The update process went fine but now I'm getting a "curious" error:
>
> Every time I make a dataset list of bam files the interfaces gives
> me following error when I try to run any tool:
>
> "Uncaught exception in exposed API method:"
>
> The error message in the galaxy.log is the following (here I just
> wanted to run hisat2, but it doesn't really matter which tool I try):
>
> 172.22.24.119 - - [19/Oct/2018:13:21:05 +0200] "POST
> /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.2/build
> <http://toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.2/build>
> HTTP/1.1" 500 -
> "http://galaxy-test.inet.dkfz-heidelberg.de/?tool_id=toolshed.g2.bx.
> psu.edu
> 
> <http://psu.edu>%2Frepos%2Fiuc%2Fhisat2%2Fhisat2%2F2.0.5.2=2.0.5.2&__identifer=froqct2i1h"
> "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:62.0) Gecko/20100101
> Firefox/62.0"
> 172.22.24.119 - - [19/Oct/2018:13:21:07 +0200] "GET
> 
> /api/histories/1cd8e2f6b131e891/contents?order=hid=dev=update_time-ge=2018-10-19T11%3A21%3A03.000Z
> HTTP/1.1" 200 -
> 
> "http://galaxy-test.inet.dkfz-heidelberg.de/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhisat2%2Fhisat2%2F2.0.5.2=2.0.5.2&__identifer=froqct2i1h;
> 
> <http://galaxy-test.inet.dkfz-heidelberg.de/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhisat2%2Fhisat2%2F2.0.5.2=2.0.5.2&__identifer=froqct2i1h>
> "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:62.0) Gecko/20100101
> Firefox/62.0"
> galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,014 Datatype
> class not found for extension 'bai', which is used as target for
> conversion from datatype 'bam'
> galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,015 Datatype
> class not found for extension 'bai', which is used as target for
> conversion from datatype 'bam'
> galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,015 Datatype
> class not found for extension 'bai', which is used as target for
> conversion from datatype 'bam'
> galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,015 Datatype
> class not found for extension 'bai', which is used as target for
> conversion from datatype 'bam'
> galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,016 Datatype
> class not found for extension 'bai', which is used as target for
> conversion from datatype 'bam'
> galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,016 Datatype
> class not found for extension 'bai', which is used as target for
> conversion from datatype 'bam'
> galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,016 Datatype
> class not found for extension 'bai', which is used as target for
> conversion from datatype 'bam'
> galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,019 Datatype
> class not found for extension 'bai', which is used as target for
> conversion from datatype 'bam'
> galaxy.web.framework.decorators ERROR 2018-10-19 13:21:08,038
> Uncaught exception in exposed API method:
> Traceback (most recent call last):
>   File
> "/opt/galaxy/galaxy/lib/galaxy/web/framework/decorators.py", line
> 281, in decorator
>     rval = func(self, trans, *args, **kwargs)
>   File
> "/opt/galaxy/galaxy/lib/galaxy/webapps/galaxy/api/tools.py", line
> 113, in build
>     return tool.to_json(trans, kwd.get('inputs', kwd))
>   File "/opt/galaxy/galaxy/lib/galaxy/tools/__init__.py", line
> 1883, in to_json
>     self.populate_model(request_context, self.inputs,
> state_inputs, tool_model['inputs'])
>   File "/opt/galaxy/galaxy/lib/galaxy/tools/__init__.py", line
> 1933, in populate_model
>     tool_dict = input.to_dict(request_context)
>   File
> "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py", line
> 701, in to_dict
>     cond_dict["cases"] = list(map(nested_to_dict, self.cases))
>   File
> "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py", line
> 699, in nested_to_dict

[galaxy-dev] Error after creating dataset list of bam files in v18.05

2018-10-23 Thread Previti

alaxy/tools/parameters/grouping.py",
line 719, in to_dict
    when_dict["inputs"] = list(map(input_to_dict, self.inputs.values()))
  File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py",
line 717, in input_to_dict
    return input.to_dict(trans)
  File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line
2005, in to_dict
    d = super(DataCollectionToolParameter, self).to_dict(trans)
  File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line
227, in to_dict
    tool_dict['value'] =
self.value_to_basic(self.get_initial_value(trans, other_values),
trans.app, use_security=True)
  File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line
1524, in get_initial_value
    if dataset_collection_matcher.hdca_match(hdca):
  File
"/opt/galaxy/galaxy/lib/galaxy/tools/parameters/dataset_matcher.py",
line 225, in hdca_match
    converted_ext, _ =
datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension,
formats)
  File "/opt/galaxy/galaxy/lib/galaxy/datatypes/registry.py", line 891,
in find_conversion_destination_for_dataset_by_extensions
    self.log.warning("Datatype class not found for extension '%s', which
is used as target for conversion from datatype '%s'" % (convert_ext,
dataset.ext))
AttributeError: 'NoneType' object has no attribute 'ext'


Has anybody dealt with this issue before?
Cheers and thanks,

Christopher


-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
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Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
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[galaxy-dev] Error after creating dataset list of bam files in v18.05

2018-10-19 Thread Previti

y/lib/galaxy/tools/parameters/grouping.py",
line 719, in to_dict
    when_dict["inputs"] = list(map(input_to_dict, self.inputs.values()))
  File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py",
line 717, in input_to_dict
    return input.to_dict(trans)
  File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line
2005, in to_dict
    d = super(DataCollectionToolParameter, self).to_dict(trans)
  File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line
227, in to_dict
    tool_dict['value'] =
self.value_to_basic(self.get_initial_value(trans, other_values),
trans.app, use_security=True)
  File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line
1524, in get_initial_value
    if dataset_collection_matcher.hdca_match(hdca):
  File
"/opt/galaxy/galaxy/lib/galaxy/tools/parameters/dataset_matcher.py",
line 225, in hdca_match
    converted_ext, _ =
datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension,
formats)
  File "/opt/galaxy/galaxy/lib/galaxy/datatypes/registry.py", line 891,
in find_conversion_destination_for_dataset_by_extensions
    self.log.warning("Datatype class not found for extension '%s', which
is used as target for conversion from datatype '%s'" % (convert_ext,
dataset.ext))
AttributeError: 'NoneType' object has no attribute 'ext'


Has anybody dealt with this issue before?
Cheers and thanks,

Christopher


-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


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Re: [galaxy-dev] Issue with deseq2

2018-09-18 Thread Previti, Christopher

Thanks a lot!
I got it to work exactly as you said.
Cheers,
Christopher

On Sep 18, 2018, at 15:56, Marius van den Beek 
mailto:m.vandenb...@gmail.com>> wrote:

Hi Christopher,

due to the old version of Galaxy you need to manually update Conda (conda 
update conda)
and explicitly set the current channel order in your galaxy.ini file, this 
should be
conda_ensure_channels = iuc,conda-forge,bioconda,defaults

With these set you can remove the exisiting conda environment for deseq2
(conda env remove -n 
mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101)
and then re-install deseq2.
Once you update to a newer Galaxy version you can comment the 
conda_ensure_channels setting again
and continue using the default channel order that Galaxy ships.

Hope that helps,
Marius


On Tue, 18 Sep 2018 at 12:18, Christopher Previti 
mailto:christopher.prev...@dkfz-heidelberg.de>>
 wrote:
Dear all,

I have been trying to get deseq2 (latest version 17,  2018-09-05 from iuc; we 
are still running on galaxy version 17.09) to work properly but to no avail. 
Older versions have other errors, I have focused on the latest version.

I get this cryptic error when I run it:

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R:
 symbol lookup error:
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6:
 undefined symbol: PC

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R:
 symbol lookup error:
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6:
 undefined symbol: PC


Does anybody know what to do about this?

Thanks and best regards,

Christopher

--
Dr. Christopher Previti
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661
christopher.prev...@dkfz.de<http://www.dkfz.de/>
www.dkfz.de<http://www.dkfz.de/>
Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschlie?lich f?r die Personen 
bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur f?r den/die Empf?nger bestimmte 
Informationen enthalten. Sollten Sie nicht
der bestimmungsgem??e Empf?nger sein, kontaktieren Sie bitte den Absender und 
l?schen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist 
untersagt.

___
Please keep all replies on the list by using "reply all"
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___
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[galaxy-dev] Issue with deseq2

2018-09-18 Thread Christopher Previti

Dear all,

I have been trying to get deseq2 (latest version 17, 2018-09-05 from
iuc; we are still running on galaxy version 17.09) to work properly but
to no avail. Older versions have other errors, I have focused on the
latest version.

I get this cryptic error when I run it:

/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/R:
symbol lookup error:
/opt/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-dbc1e05d0db06d983572e7eca0df68af225d8f398b6e11dd4d586075518c4101/lib/R/bin/exec/../../lib/../../libreadline.so.6:
undefined symbol: PC

Does anybody know what to do about this?

Thanks and best regards,

Christopher

--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.

___
Please keep all replies on the list by using "reply all"
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[galaxy-dev] Issue with deseq2

2018-09-18 Thread Previti

Dear all,

I get this cryptic error when I run it:

Does anybody know what to do about this?

Thanks and best regards,

Christopher

--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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

Re: [galaxy-dev] Salmon references and data manager

2018-09-07 Thread Previti

Yeah, I got confused about the data tables. Sorry about this. I too
would keep the transcriptome indices separate from the reference
genomes, it just makes sense.

 @Ignacio, I found that you need insert the following (in red)

if not os.path.exists( target_directory ):

    os.mkdir( target_directory )

args = ['salmon','index']

in order for anything to happen.

I think that's it...but I'll test some more.

Best regards,

Christopher


On 09/07/2018 10:46 AM, Ignacio EGUINOA wrote:
> Hi Christopher and Björn,
>
> I have some comments about this because I also came up with these
> questions some time ago...
>
> 
>
> *From: *"Björn Grüning" 
> *To: *"Previti" ,
> "galaxy-dev" 
> *Sent: *Friday, September 7, 2018 9:56:41 AM
> *Subject: *Re: [galaxy-dev] Salmon references and data manager
>
> Hi Christopher!
>
> > Dear Björn,
> >
> > I just installed Salmon on our Galaxy instance and I have a
> couple of
> > basic questions.
>
> Sure, thanks for getting in touch!
>
> > Currently the reference transcriptomes are put in the same data
> table as
> > the genomes, would it be of interest to separate this and give the
> >
> > transcriptomes their own table? I could probably try to do this...
>
> That I don't understand?
> Salmon is using this one here, isn't it?
>
> 
> https://github.com/bgruening/galaxytools/blob/master/tools/salmon/salmon.xml#L233
>
> What he means, I think, is the table to build the index from. Data
> managers that take a transcriptome as input get it from the all_fasta
> table, I think that is what he means by the genomes table.
> As I said at some point I also thought it may be useful to have a
> separate table (e.g all_transcriptomes) so that the genome and
> transcriptome entries of the same build don't get mixed. I think it
> would be good to have a way of listing only the transcriptomes from
> the all_gff but that would requiere some kind of standard on the
> naming to filter. We had this in our instance at some point but didn't
> help at all so I just modified the data manger to use the all_fasta
> and that is what I published.
> So, @Christopher ...having a separate table is not the solution
> although it would be easier for the GUI. For now just giving the
> entries a descriptive name to indicate the entries correspond to a
> transcriptome is enough and works ok for us. In any case this is not
> for users and at least for us its all handled through the API so,
> again, it's just a matter of taking care of the entries names and you
> are fine with using the all_fasta table.
>
>
>
> > There is a data manager available that unfortunately has a bug.
> We fixed
> > that and it now populates the reference genome data table.
>
> Do you mean this one?
>
> https://github.com/ieguinoa/data_manager_salmon_index_builder
>
> > I would probably modify this as well use the new table. Could
> this be
> > useful? I'm not sure how to proceed...would I give you the modified
> > Salmon wrapper for inclusion in the package?
>
> If you can, please feel free to create PRs to the repositories, so we
> can all reviewed it. And then, when we merge, it gets automatically
> updated to the Tool Shed :)
>
> As Björn said, if that's the one you are talking about please create a
> PR or an isssue or contact me.
>
> Cheers,
> Ignacio
>
> Thanks!
> Bjoern
>
> > Best regards,
> >
> > Christopher
> >
> >
> > --
> > *Dr. Christopher Previti*
> > Genomics and Proteomics Core Facility
> > High Throughput Sequencing (W190)
> > Bioinformatician
> >
> > German Cancer Research Center (DKFZ)
> > Foundation under Public Law
> > Im Neuenheimer Feld 580
> > 69120 Heidelberg
> > Germany
> > Room: B2.102 (INF580/TP3)
> > Phone: +49 6221 42-4661
> >
> > christopher.prev...@dkfz.de <http://www.dkfz.de/>
> > www.dkfz.de <http://www.dkfz.de/>
> >
> > Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> > VAT-ID No.: DE143293537
> >
> > Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
> > Personen bestimmt, an die sie adressiert ist.
> > Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
> > Informationen enthalten. Sollten Sie nicht
> > der bestimmungsgemäß

[galaxy-dev] Setting up Galaxy Reports

2018-08-31 Thread Previti

Dear Hans-Rudolf and list participants,

We would like to set up the galaxy reports tool on our version 17.09
instance and we succeeded partially after modifying the "reports.yml" to
point to our postgresql database.

The webpage is generated, with all the stats, but looks very basic and
the appropriate style-sheets are probably not found...

Any advise on how to set this up properly would be very welcome.

Best regards,

Christopher

On 08/17/2017 04:56 PM, Hans-Rudolf Hotz wrote:
> Hi Evan
>
> I assume you are talking about the 'reports' tool?
>
> Have a look here:
>
> https://galaxyproject.org/admin/usage-reports/
> https://docs.galaxyproject.org/en/latest/admin/reports.html
>
> Additional (system) information about each executed job can be logged
> by activating plugins in the "./config/job_metrics_conf.xml" file.
>
> https://galaxyproject.org/admin/config/job-metrics/
>
>
> Hope this helps
> Regards, Hans-Rudolf
>
>
>
> On 08/17/2017 04:25 PM, evan clark wrote:
>> I remember there previously being an additional tool that ran on a
>> different port from galaxy that allowed for monitoring of performance
>> and jobs running. Is this tool still packaged with galaxy and if so how
>> can it be activated.
>> ___
>> 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/
> ___
> 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/

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.

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[galaxy-dev] Workflow renaming problem for tool with multiple outputs (Galaxy version 17.09)

2018-05-23 Thread Previti

Hi everybody,

I'd like to fix this bug in our local galaxy instance...it's with regard
to the erroneous renaming of output files, when there are multiple
outputs available.

The relevant ticket is the following:

https://github.com/galaxyproject/galaxy/pull/5021

Unfortunately a quick update to the newest Galaxy version is not
possible for us at the moment.

Any tips on how I could do this?

Thanks and best regards,

Christopher Previti

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


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[galaxy-dev] Purging "Monitor installing repositories"

2018-05-23 Thread Previti

Dear all,

I've been having an issue with the "Monitor installing repositories"
page. There is a whole list of tools that were not installed properly
(usually they got interrupted for some reason) and they aren't being
removed.

Is there a way to purge this list manually?

Thanks and best regards,

Christopher Previti

<http://dkfzgalaxy.inet.dkfz-heidelberg.de/admin_toolshed/monitor_repository_installation?installing_repository_ids=17912123b7aa6af3,c2f15bb285119094,4a31abf1f877a79d,b1208393f3608833,d796ca8e1687a54b,53fb5c5113d9beb7,6df0b7b066ddc4c9,9c18ad129e678b2a,06cf32e9aa8aad75,34c3e3c01e1a37f4,e96c6ce43a3d239a,96aaea51084561ca,ea3d97b57366b47f,eff20c5ba6bf6f87,61612e311c53402a,a40b6b1bc78914d2,d3f11f9fc62015d5,b425b2361a02d64e,9fc09fe7b5ac6411,47b494785f085395,77efbec71a7e1a47,5bdd2b702d04bb52>

--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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

Re: [galaxy-dev] Trackster ownership issue

2018-05-16 Thread Previti

Ah, no I was wrong, they don't have the same email, they each have a
separate account , i.e. cour...@dkfz.de, cour...@dkfz.de etc...

The issue is that I set it up so all files associated with these
accounts (everything in the histories) are stored in the same directory.

That's why they could see each other's files in trackster, so it's not
really an issue.

Thanks for answering! This is the first time I did a Galaxy Course and
I'm still optimizing a bit

Christopher


On 05/16/2018 03:55 PM, Dannon Baker wrote:
> Oh that's interesting.  It shouldn't be allowed to create multiple
> users with the same email address, unless you've changed that -- can
> you elaborate on what you've done?
>
> -Dannon
>
> On Wed, May 16, 2018 at 9:48 AM Previti
> <christopher.prev...@dkfz-heidelberg.de
> <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>
> Hi,
>
> I just implemented a couple of features (impersonate/delete users)
> that I'm going to use for troubleshooting due to the fact that
> this might be an issue that is specific to us.
>
> I think it might be an issue with the user-accounts
> themselves...they're "artificial" in a sense that they are called
> "course1" through "course10" (as username and password) and all
> associated with the same email address...
>
> Could this be problematic in general?
>
> Cheers,
> Christopher
>  
> On 05/16/2018 02:35 PM, Dannon Baker wrote:
>> I definitely have not seen this before, and am not able to
>> reproduce it on my local instance.  Can you provide a screenshot
>> of what you're seeing, and the organization of the histories that
>> are being sourced for the incorrect datasets?
>>
>> On Wed, May 16, 2018 at 7:25 AM Previti
>> <christopher.prev...@dkfz-heidelberg.de
>> <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>>
>> Dear all,
>>
>> I'm having a strange issue with Trackster in our Galaxy
>> implementation.
>>
>> Users seem to be able to upload files ("Add Datasets")
>> from*all *histories of all users, regardless of ownership.
>>
>> ...is this something that has been observed before...? How do
>> I stop this from happening?
>>
>> Thanks and best regards,
>>
>> Christopher
>>
>> -- 
>> *Dr. Christopher Previti*
>> Genomics and Proteomics Core Facility
>> High Throughput Sequencing (W190)
>> Bioinformatician
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 580
>> 69120 Heidelberg
>> Germany
>> Room: B2.102 (INF580/TP3)
>> Phone: +49 6221 42-4661
>>
>> christopher.prev...@dkfz.de <http://www.dkfz.de/>
>> www.dkfz.de <http://www.dkfz.de/>
>>
>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef
>> Puchta
>> VAT-ID No.: DE143293537
>>
>> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich
>> für die Personen bestimmt, an die sie adressiert ist.
>> Sie kann vertrauliche und/oder nur für den/die Empfänger
>> bestimmte Informationen enthalten. Sollten Sie nicht
>> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte
>> den Absender und löschen Sie die Mitteilung.
>> Jegliche unbefugte Verwendung der Informationen in dieser
>> Nachricht ist untersagt.
>>
>>
>> ___
>> 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/
>>
>
> -- 
> *Dr. Christopher Previti*
> Genomics and Proteomics Core Facility
> High Throughput Sequencing (W190)
> Bioinformatician
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 580
> 69120 Heidelberg
> Germany
> Room: B2.102 (INF580/TP3)
> Phone: +49 6221 42-4661
>
> christopher.prev...@dkfz.de <http://www.dkfz.de/>
> www.dkfz.de <http://www.dkfz.de/>

Re: [galaxy-dev] Trackster ownership issue

2018-05-16 Thread Previti

Hi,

I just implemented a couple of features (impersonate/delete users) that
I'm going to use for troubleshooting due to the fact that this might be
an issue that is specific to us.

I think it might be an issue with the user-accounts themselves...they're
"artificial" in a sense that they are called "course1" through
"course10" (as username and password) and all associated with the same
email address...

Could this be problematic in general?

Cheers,
Christopher

On 05/16/2018 02:35 PM, Dannon Baker wrote:
> I definitely have not seen this before, and am not able to reproduce
> it on my local instance.  Can you provide a screenshot of what you're
> seeing, and the organization of the histories that are being sourced
> for the incorrect datasets?
>
> On Wed, May 16, 2018 at 7:25 AM Previti
> <christopher.prev...@dkfz-heidelberg.de
> <mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:
>
> Dear all,
>
> I'm having a strange issue with Trackster in our Galaxy
> implementation.
>
> Users seem to be able to upload files ("Add Datasets") from*all
> *histories of all users, regardless of ownership.
>
> ...is this something that has been observed before...? How do I
> stop this from happening?
>
> Thanks and best regards,
>
> Christopher
>
> -- 
> *Dr. Christopher Previti*
> Genomics and Proteomics Core Facility
> High Throughput Sequencing (W190)
> Bioinformatician
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 580
> 69120 Heidelberg
> Germany
> Room: B2.102 (INF580/TP3)
> Phone: +49 6221 42-4661
>
> christopher.prev...@dkfz.de <http://www.dkfz.de/>
> www.dkfz.de <http://www.dkfz.de/>
>
> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> VAT-ID No.: DE143293537
>
> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für
> die Personen bestimmt, an die sie adressiert ist.
> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
> Informationen enthalten. Sollten Sie nicht
> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
> Absender und löschen Sie die Mitteilung.
> Jegliche unbefugte Verwendung der Informationen in dieser
> Nachricht ist untersagt.
>
>
> ___
> 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/
>

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.

___
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/

[galaxy-dev] Trackster ownership issue

2018-05-16 Thread Previti

Dear all,

I'm having a strange issue with Trackster in our Galaxy implementation.

Users seem to be able to upload files ("Add Datasets") from*all
*histories of all users, regardless of ownership.

...is this something that has been observed before...? How do I stop
this from happening?

Thanks and best regards,

Christopher

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
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/

Re: [galaxy-dev] Galaxy Cleanup

2018-04-27 Thread Previti

Thanks! Super useful!

Cheers,

Christopher


On 04/27/2018 04:12 PM, Nicola Soranzo wrote:
> See also:
>
> https://galaxyproject.github.io/training-material/topics/admin/tutorials/monitoring-maintenance/slides.html
>
>
> Cheers,
> Nicola
>
> On 27/04/18 15:05, Hans-Rudolf Hotz wrote:
>> Hi Christopher
>>
>>
>> It depends on the setting of "cleanup_job" ('always', 'onsuccess',
>> 'never'), whether the temporary files are cleaned up or not. Though,
>> to be honest, I don't know, if this setting as any influence, when
>> you 'delete' a job.
>>
>> For the quotas, only dataset in the histories are counted
>>
>> The temporary files are very handy for debugging, so I have
>> 'onsuccess' on our production server and 'never' on our development
>> server. I just regularly check the total size of the working
>> directories and do the clean up manually
>>
>>
>> Regards, Hans-Rudolf
>>
>>
>>
>>
>> On 04/27/2018 01:51 PM, Previti wrote:
>>> Hi everybody,
>>>
>>> I have a hopefully basic questions regarding temporary output files.
>>>
>>> A user was generating >4TB output files via the program bedtools
>>> intersectbed. The jobs were cancelled, but I still see the (temporary)
>>> output files that were generated.
>>>
>>> Does Galaxy clean these up? Does it do this regularly?
>>>
>>> Would a quota prevent something like this from happening again or would
>>> the jobs have to finish before being "counted"?
>>>
>>> Thanks and best regards,
>>>
>>> Christopher
>>>
>>> -- 
>>> *Dr. Christopher Previti*
>>> Genomics and Proteomics Core Facility
>>> High Throughput Sequencing (W190)
>>> Bioinformatician
>>>
>>> German Cancer Research Center (DKFZ)
>>> Foundation under Public Law
>>> Im Neuenheimer Feld 580
>>> 69120 Heidelberg
>>> Germany
>>> Room: B2.102 (INF580/TP3)
>>> Phone: +49 6221 42-4661
>>>
>>> christopher.prev...@dkfz.de <http://www.dkfz.de/>
>>> www.dkfz.de <http://www.dkfz.de/>
>>>
>>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
>>> VAT-ID No.: DE143293537
>>>
>>> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
>>> Personen bestimmt, an die sie adressiert ist.
>>> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
>>> Informationen enthalten. Sollten Sie nicht
>>> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
>>> Absender und löschen Sie die Mitteilung.
>>> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
>>> untersagt.
>>>
>>>
>>>
>>>
>>> ___
>>> 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/
>>>
>> ___
>> 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/
>

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
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/

[galaxy-dev] Galaxy Cleanup

2018-04-27 Thread Previti

Hi everybody,

I have a hopefully basic questions regarding temporary output files.

A user was generating >4TB output files via the program bedtools
intersectbed. The jobs were cancelled, but I still see the (temporary)
output files that were generated.

Does Galaxy clean these up? Does it do this regularly?

Would a quota prevent something like this from happening again or would
the jobs have to finish before being "counted"?

Thanks and best regards,

Christopher

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
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/

[galaxy-dev] Samtools running on submit-node and as a slurm job

2018-04-24 Thread Previti

Dear all,

We found something strange with our Galaxy instance...

Our Galaxy server is configured as a submit node using slurm to submit
to our cluster.

This works fine for the most part, but today we saw a samtools index job
running "locally" on the submit node instead of a  cluster node.

Is there any way of stopping this behavior? The submit nodes are not
configured for data-intensive computation and everything runs
significantly slower.

I was running bamtools (splitting a bam-file into mapped into unmapped)
at the time and the output bam-files were being indexed. 

Thanks and best regards,

Christopher

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
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/

[galaxy-dev] Error during FASTQ preview

2018-03-13 Thread Previti

Dear all,

I've recently had following error occur on our local Galaxy instance.

Every time I want to preview a fastq file it gives this:

Content Encoding Error

The page you are trying to view cannot be shown because it uses an
invalid or unsupported form of compression.

    Please contact the website owners to inform them of this problem.

Any idea how to solve this...? This is the first time I'm seeing itI
tried changing the data type multiple times (fastq, fastq.gz,
fastqsanger...etc) but this doesn't get rid of it.

Best regards,

Christopher Previti



-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
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/

[galaxy-dev] show tool errors admin interface

2017-09-28 Thread Previti

Dear all,

Does anybody know how to configure galaxy to actually show errors under
the "show tool errors" section of the admin interface?

I can't find any infos about this...we're running version 17.05.

Thanks and best regards,

Christopher

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
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/

[galaxy-dev] Bug in "View all histories", history "disappears"

2017-09-27 Thread Previti

Dear all,

I noticed a bug in Galaxy (17.05), specifically when using "View all
histories"  to switch between different histories.
It happened to me multiple times that the history I switched away from
was not shown anymore.
Searching for the history by name made it show up again, but still not
ideal.
I have about 10 histories that I cycle through on a regular basis.
Doesn't the system support that many?

Cheers,
Christopher


-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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[galaxy-dev] Bugfix - Summary Statistics Script - Python incompatibility

2017-07-14 Thread Previti

Dear all,

I hope this can be of use to somebody...

We were having problems with the Summary Statistics Tools

/galaxy/tools/stats/gsummary.py

 As indicated there is a dependency on rpy2 (Version 2.7.8), which
requires python 3.5 and comes into conflict with the qsummary.py which
uses 2.*

Change 

Line 63:  tmp_file = tempfile.NamedTemporaryFile( 'w+b' )

to

 tmp_file = tempfile.NamedTemporaryFile( 'w+' )

Then it'll work.

Cheers,

Christopher

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
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Re: [galaxy-dev] Java memory requirements for Picard index?

2017-07-11 Thread Previti

Dear Börn,

Sorry for the late response but thanks!

I'll look into it,

Christopher



On 07/07/2017 06:36 PM, Björn Grüning wrote:
> Hi Christopher,
>
> you can increase the JVM memory options via the job_conf.xml file for a
> particular tool.
>
> Hope this helps,
> Bjoern
>
> Am 06.07.2017 um 13:05 schrieb Previti:
>> Dear all,
>> I seemly have a java issue (out of memory) when trying to construct a
>> picard index for the rat (rn6) genome build using the
>> picard_index_builder_data_manager.
>> This is strange because other, bigger genomes have not presented any
>> problems...
>>
>> Does anybody have any suggestions?
>>
>> Cheers,
>> Christopher Previti
>>
>> Fatal error: Exit code 1 ()
>> [Thu Jul 06 08:26:48 UTC 2017] picard.sam.CreateSequenceDictionary 
>> REFERENCE=/opt/galaxy/galaxy/database/jobs_directory/000/978/dataset_1974_files/rn6.fa
>>  OUTPUT=rn6.dictTRUNCATE_NAMES_AT_WHITESPACE=true 
>> NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false 
>> VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=50 
>> CREATE_INDEX=false CREATE_MD5_FILE=false 
>> GA4GH_CLIENT_SECRETS=client_secrets.json
>> [Thu Jul 06 08:26:48 UTC 2017] Executing as 
>> gal...@xgs-node071.xgs.dkfz-heidelberg.de on Linux 3.10.0-514.el7.x86_64 
>> amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 2.7.1-SNAPSHOT
>> [Thu Jul 06 08:26:49 UTC 2017] picard.sam.CreateSequenceDictionary done. 
>> Elapsed time: 0.03 minutes.
>> Runtime.totalMemory()=1051721728
>> To get help, see 
>> http://broadinstitute.github.io/picard/index.html#GettingHelp
>> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
>>  at 
>> htsjdk.samtools.reference.FastaSequenceFile.readSequence(FastaSequenceFile.java:151)
>>  at 
>> htsjdk.samtools.reference.FastaSequenceFile.nextSequence(FastaSequenceFile.java:81)
>>  at 
>> picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:156)
>>  at 
>> picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:137)
>>  at 
>> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
>>  at 
>> picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
>>  at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
>> Error building index.
>>
>>
>>
>>
>>
>>
>>
>> -- 
>> *Dr. Christopher Previti*
>> Genomics and Proteomics Core Facility
>> High Throughput Sequencing (W190)
>> Bioinformatician
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 580
>> 69120 Heidelberg
>> Germany
>> Room: B2.102 (INF580/TP3)
>> Phone: +49 6221 42-4434
>>
>> christopher.prev...@dkfz.de <http://www.dkfz.de/>
>> www.dkfz.de <http://www.dkfz.de/>
>>
>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
>> VAT-ID No.: DE143293537
>>
>> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
>> Personen bestimmt, an die sie adressiert ist.
>> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
>> Informationen enthalten. Sollten Sie nicht
>> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
>> Absender und löschen Sie die Mitteilung.
>> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
>> untersagt.
>>
>>
>>
>>
>> ___
>> 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/
>>

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] DeepTools python dependency issues?

2017-07-05 Thread Previti

It worked, thanks again!


On 07/05/2017 03:37 PM, Previti wrote:
>
> Thanks, I'll give it a try!
>
> Cheers,
>
> Christopher
>
>
> On 07/05/2017 03:13 PM, Ignacio EGUINOA wrote:
>> Hi
>>
>> I had the same problem with deeptools, I guess the original bzip2
>> package (in anaconda) was built incorrectly because it contains
>> libbz2.a instead of the shared library libbz2.so.1.0
>> Not sure what is the problem because the recipe seems to be ok
>> (https://github.com/ContinuumIO/anaconda-recipes/blob/master/bzip2/build.sh)
>> I didn 't want to change anything out of the conda environment so
>> what I did for the moment is build the bzip2 package with shared
>> libraries locally:
>>
>> Download and extract http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
>> make -f Makefile-libbz2_so
>> and then copy the libbz2.so that it creates to deeptools_env/lib
>>
>> I'm just mentioning this but of course is not the correct solution,
>> it is just so that you can solve it in the meantime while we wait for
>> someone to explain what can be wrong with the bzip2 package.
>>
>> cheers,
>> Ignacio
>>
>> 
>>
>> *From: *"Previti" <christopher.prev...@dkfz-heidelberg.de>
>> *To: *"galaxy-dev" <galaxy-dev@lists.galaxyproject.org>
>> *Sent: *Wednesday, July 5, 2017 2:51:32 PM
>> *Subject: *[galaxy-dev] DeepTools python dependency issues?
>>
>> Dear all,
>>
>> I was wondering if anybody has seen the following error after
>> installing deeptools in the galaxy interface:
>>
>> Fatal error: Exit code 1 ()
>> Traceback (most recent call last):
>>   File 
>> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/bin/plotCoverage",
>>  line 4, in 
>> from deeptools.plotCoverage import main
>>   File 
>> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/plotCoverage.py",
>>  line 15, in 
>> import deeptools.countReadsPerBin as countR
>>   File 
>> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/countReadsPerBin.py",
>>  line 9, in 
>> import deeptools.utilities
>>   File 
>> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/utilities.py",
>>  line 3, in 
>> import pysam
>>   File 
>> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/pysam/__init__.py",
>>  line 5, in 
>> from pysam.libchtslib import *
>> ImportError: libbz2.so.1.0: cannot open shared object file: No such file 
>> or directory
>>
>>
>> Has anybody encountered this error before and were you able to
>> resolve it?
>>
>> Thanks and best regards,
>>
>> Christopher Previti
>>
>>  
>>
>> -- 
>> *Dr. Christopher Previti*
>> Genomics and Proteomics Core Facility
>> High Throughput Sequencing (W190)
>> Bioinformatician
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 580
>> 69120 Heidelberg
>> Germany
>> Room: B2.102 (INF580/TP3)
>> Phone: +49 6221 42-4434
>>
>> christopher.prev...@dkfz.de <http://www.dkfz.de/>
>> www.dkfz.de <http://www.dkfz.de/>
>>
>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
>> VAT-ID No.: DE143293537
>>
>> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für
>> die Personen bestimmt, an die sie adressiert ist.
>> Sie kann vertrauliche und/oder nur für den/die Empfänger
>> bestimmte Informationen enthalten. Sollten Sie nicht
>> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
>> Absender und löschen Sie die Mitteilung.
>> Jegliche unbefugte Verwendung der Informationen in dieser
>> Nachricht ist untersagt.
>>
>>
>>
>> ___
>> 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.

Re: [galaxy-dev] DeepTools python dependency issues?

2017-07-05 Thread Previti

Thanks, I'll give it a try!

Cheers,

Christopher


On 07/05/2017 03:13 PM, Ignacio EGUINOA wrote:
> Hi
>
> I had the same problem with deeptools, I guess the original bzip2
> package (in anaconda) was built incorrectly because it contains
> libbz2.a instead of the shared library libbz2.so.1.0
> Not sure what is the problem because the recipe seems to be ok
> (https://github.com/ContinuumIO/anaconda-recipes/blob/master/bzip2/build.sh)
> I didn 't want to change anything out of the conda environment so what
> I did for the moment is build the bzip2 package with shared libraries
> locally:
>
> Download and extract http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
> make -f Makefile-libbz2_so
> and then copy the libbz2.so that it creates to deeptools_env/lib
>
> I'm just mentioning this but of course is not the correct solution, it
> is just so that you can solve it in the meantime while we wait for
> someone to explain what can be wrong with the bzip2 package.
>
> cheers,
> Ignacio
>
> ----
>
> *From: *"Previti" <christopher.prev...@dkfz-heidelberg.de>
> *To: *"galaxy-dev" <galaxy-dev@lists.galaxyproject.org>
> *Sent: *Wednesday, July 5, 2017 2:51:32 PM
> *Subject: *[galaxy-dev] DeepTools python dependency issues?
>
> Dear all,
>
> I was wondering if anybody has seen the following error after
> installing deeptools in the galaxy interface:
>
> Fatal error: Exit code 1 ()
> Traceback (most recent call last):
>   File 
> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/bin/plotCoverage",
>  line 4, in 
> from deeptools.plotCoverage import main
>   File 
> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/plotCoverage.py",
>  line 15, in 
> import deeptools.countReadsPerBin as countR
>   File 
> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/countReadsPerBin.py",
>  line 9, in 
> import deeptools.utilities
>   File 
> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/deeptools/utilities.py",
>  line 3, in 
> import pysam
>   File 
> "/opt/galaxy/galaxy/database/dependencies/_conda/envs/__deeptools@2.5.1/lib/python3.6/site-packages/pysam/__init__.py",
>  line 5, in 
> from pysam.libchtslib import *
> ImportError: libbz2.so.1.0: cannot open shared object file: No such file 
> or directory
>
>
> Has anybody encountered this error before and were you able to
> resolve it?
>
> Thanks and best regards,
>
> Christopher Previti
>
>  
>
> -- 
> *Dr. Christopher Previti*
> Genomics and Proteomics Core Facility
> High Throughput Sequencing (W190)
> Bioinformatician
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 580
> 69120 Heidelberg
> Germany
> Room: B2.102 (INF580/TP3)
> Phone: +49 6221 42-4434
>
> christopher.prev...@dkfz.de <http://www.dkfz.de/>
> www.dkfz.de <http://www.dkfz.de/>
>
> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> VAT-ID No.: DE143293537
>
> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für
> die Personen bestimmt, an die sie adressiert ist.
> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
> Informationen enthalten. Sollten Sie nicht
> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
> Absender und löschen Sie die Mitteilung.
> Jegliche unbefugte Verwendung der Informationen in dieser
> Nachricht ist untersagt.
>
>
>
> _______
> 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/
>

-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.prev...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Re: [galaxy-dev] Fwd: Fwd: Usegalaxy.org Data Rsync Connection refused

2017-01-17 Thread Christopher Previti


Thanks a lot, it works now!


Am 17.01.2017 um 16:45 schrieb Nate Coraor:

Hi Christopher,

It's been up for a while now. The IP address is now 128.118.250.24 - 
is it still resolving to 128.118.250.10 for you?


--nate

On Mon, Jan 16, 2017 at 3:01 AM, Christopher Previti 
<christopher.prev...@dkfz-heidelberg.de 
<mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:


Hi Nate,
Happy New Year (though belated)! I was wondering if you managed to
get the rsync server to work...it still gives me the same error
message I received
the last time I tried.

Cheers and thanks!
Christopher



Am 19.12.2016 um 18:30 schrieb Nate Coraor:

Hi Christopher,

It's currently down due to a hardware failure. I hope to have it
back up within the week. Sorry for the inconvenience.

Thanks,
--nate

On Wed, Dec 14, 2016 at 3:14 AM, Christopher Previti
<christopher.prev...@dkfz-heidelberg.de
<mailto:christopher.prev...@dkfz-heidelberg.de>> wrote:

Dear all,

I was wondering if anybody was able to get the rsync server
datacache.g2.bx.psu.edu <http://datacache.g2.bx.psu.edu> to
work? Have there been non-documented changes?

We still get following messages:

rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX
<http://datacache.g2.bx.psu.edu/indexes/phiX> .
rsync: failed to connect to datacache.g2.bx.psu.edu
<http://datacache.g2.bx.psu.edu> (128.118.250.10): Connection
refused (111)
rsync error: error in socket IO (code 10) at
clientserver.c(128) [Receiver=3.1.1]

My colleague Georgios Nikolis and I are working on a local
Galaxy installation at the DKFZ and would really like to use
the pre-built indices.

    Cheers,

Christopher Previti



 Weitergeleitete Nachricht 
Betreff:Fwd: [galaxy-dev] Usegalaxy.org Data Rsync
Connection refused
Datum:  Tue, 13 Dec 2016 13:46:48 +0100
Von:Georgios Nikolis <g.niko...@dkfz-heidelberg.de>
<mailto:g.niko...@dkfz-heidelberg.de>
An: Christopher Previti
<christopher.prev...@dkfz-heidelberg.de>
<mailto:christopher.prev...@dkfz-heidelberg.de>





*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659 <tel:+49%206221%20424659>

g.niko...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef
Puchta
VAT-ID No.: DE143293537





 Forwarded Message 
Subject:[galaxy-dev] Usegalaxy.org Data Rsync Connection
refused
Date:   Fri, 28 Oct 2016 15:23:14 +0200
From:   Georgios Nikolis <g.niko...@dkfz-heidelberg.de>
<mailto:g.niko...@dkfz-heidelberg.de>
To: galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>
<galaxy-dev@lists.galaxyproject.org>
<mailto:galaxy-dev@lists.galaxyproject.org>



Dear all,
we are currently working on setting up a new local Galaxy
installation and I would like to obtain the genome reference
data available on the public Galaxy instance. I am following
the instructions on the Wiki page
(https://wiki.galaxyproject.org/Admin/UseGalaxyRsync
<https://wiki.galaxyproject.org/Admin/UseGalaxyRsync>), but I
can't seem to be able to access datacache.g2.bx.psu.edu
<http://datacache.g2.bx.psu.edu> via rsync.
rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX
<http://datacache.g2.bx.psu.edu/indexes/phiX> .
rsync: failed to connect to datacache.g2.bx.psu.edu
<http://datacache.g2.bx.psu.edu> (128.118.250.10): Connection
refused (111)
rsync error: error in socket IO (code 10) at
clientserver.c(128) [Receiver=3.1.1]

Does anyone know if the URL has changed in the meantime? Is
there any alternative way to access this data?

Thanks in advance!

Best regards,
Georgios


-- 
*Georgios Nikolis*

Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659 <te

[galaxy-dev] Fwd: Fwd: Usegalaxy.org Data Rsync Connection refused

2016-12-14 Thread Christopher Previti


Dear all,

I was wondering if anybody was able to get the rsync server 
datacache.g2.bx.psu.edu to work? Have there been non-documented changes?


We still get following messages:

rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .
rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): 
Connection refused (111)
rsync error: error in socket IO (code 10) at clientserver.c(128) 
[Receiver=3.1.1]


My colleague Georgios Nikolis and I are working on a local Galaxy 
installation at the DKFZ and would really like to use the pre-built indices.


Cheers,

Christopher Previti



 Weitergeleitete Nachricht 
Betreff:Fwd: [galaxy-dev] Usegalaxy.org Data Rsync Connection refused
Datum:  Tue, 13 Dec 2016 13:46:48 +0100
Von:Georgios Nikolis <g.niko...@dkfz-heidelberg.de>
An: Christopher Previti <christopher.prev...@dkfz-heidelberg.de>





*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659

g.niko...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537





 Forwarded Message 
Subject:[galaxy-dev] Usegalaxy.org Data Rsync Connection refused
Date:   Fri, 28 Oct 2016 15:23:14 +0200
From:   Georgios Nikolis <g.niko...@dkfz-heidelberg.de>
To: 	galaxy-dev@lists.galaxyproject.org 
<galaxy-dev@lists.galaxyproject.org>




Dear all,
we are currently working on setting up a new local Galaxy installation 
and I would like to obtain the genome reference data available on the 
public Galaxy instance. I am following the instructions on the Wiki page 
(https://wiki.galaxyproject.org/Admin/UseGalaxyRsync), but I can't seem 
to be able to access datacache.g2.bx.psu.edu via rsync.

rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .
rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.250.10): 
Connection refused (111)
rsync error: error in socket IO (code 10) at clientserver.c(128) 
[Receiver=3.1.1]


Does anyone know if the URL has changed in the meantime? Is there any 
alternative way to access this data?


Thanks in advance!

Best regards,
Georgios


--
*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659

g.niko...@dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

Management Board: Prof. Dr. Michael Boutros (interim), Prof. Dr. Josef 
Puchta

VAT-ID No.: DE143293537





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