Re: [galaxy-dev] Galaxy SNPEff Display Bug (2nd Independent Report)
Hello Dannon, Thanks for resolving the issue of snpEff HTML display. It's working well with the new changeset. But the gene file link in the bottom (dataset_*.dat.genes.txt) is still in broken state, says could not find file. Any update on this? -Raj -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John David Osborne Sent: Thursday, March 08, 2012 9:34 PM To: Dannon Baker Cc: galaxy-dev@lists.bx.psu.edu; David K Crossman; Pablo; shant...@lists.bx..psu.edu Subject: Re: [galaxy-dev] Galaxy SNPEff Display Bug (2nd Independent Report) Very helpful, thank you! I don't see this option in universe_wsgi.ini, but hopefully I will when we update our galaxy. Thanks! -John On 3/8/12 9:53 AM, Dannon Baker dannonba...@me.com wrote: This was addressed in 6788:e58a87c91bc4. The reason for the initial change that's causing these display issues was to eliminate potential XSS vulnerabilities. There's now a configuration option (sanitize_all_html, which is True by default) for local instances where you can disable the extra html sanitization. -Dannon On Mar 8, 2012, at 10:33 AM, John David Osborne wrote: Hi Pablo, About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer correctly displays the HTML report in galaxy we have the exact same error. Is there a workaround for this yet? I found his original report here: http://article.gmane.org/gmane.science.biology.galaxy.user/2418 The report looks great when generated from the command line or even if the files from galaxy are copied over to a local machine and displayed. However in galaxy it appears that the supplementary data file (for example) from the original dataset_41.dat is not accessible to the main html file although I can copy it off the server. Perhaps the data file it is being called from elsewhere at this is a path related issue? The html looks for the data file in the same directory which I think is quite reasonable. I'm not sure which galaxy update broke this, but it is definitely broken and I'm guessing any efforts to display html reports in galaxy that involve other supplementary data files may be broken tooŠ. -John ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] drmaa module does not load
Hello everyone, I wanted to start the drmaa job runner and followed the instructions in the wiki, but I have this error message when I start Galaxy: galaxy.jobs ERROR 2012-03-23 15:28:49,845 Job runner is not loadable: galaxy.jobs.runners. drmaa Traceback (most recent call last): File /g/funcgen/galaxy/lib/galaxy/jobs/__init__.py, line 1195, in _load_plugin module = __import__( module_name ) ImportError: No module named drmaa I checked /g/funcgen/galaxy/lib/galaxy/jobs/runners and it contains the drmaa.py file There was no drmaa egg so I made a copy of it from our other Galaxy install but it didn't solve the problem. I don't really know where to start looking, any idea? Thanks, L-A ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] New Galaxy look from usegalaxy.org
Dear all, How do I get the new Galaxy look enabled that you see in usegalaxy.org? I have two servers on the latest galaxy-dist. regards, Leandro ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Normal that latest galaxy-dist creates shed_tools directory one level up from the galaxy-dist directory?
Dear all, Is it normal that the latest galaxy-dist creates a shed_tools directory one directory up (and outside) from the server galaxy-dist directory? best, Leandro ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Using direct upload (as SRA/ENA) in our own instance
Dear All, If i browse (outsode of Galaxy) to e.g. http://www.ebi.ac.uk/ena/data/view/SRP001343 , and click on the Galaxy links on that page, it used to be that the file got uploaded to my section of the public Galaxy instance. This was probably a bug instead of a feature, as currently it doesn't work anymore. When it did work, it was really handy, and I wondered whether there is a way I could get this working in our own instance, as an easy way to get data into our Galaxy instance outside of Galaxy. This would save users copying the URLs of data to the Upload File form. -- Jan van Haarst Assistant Researcher Bioinformatics Wageningen UR, Plant Research International Applied Bioinformatics P.O Box 167, 6700 AD, Wageningen, the Netherlands Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands ++31-317480756 msn:jan.vanhaa...@wur.nl www.pri.wur.nlhttp://www.pri.wur.nl/ www.appliedbioinformatics.wur.nlhttp://www.appliedbioinformatics.wur.nl/ www.disclaimer-uk.wur.nlhttp://www.disclaimer-uk.wur.nl/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] functional test failures
Hi Anne, We're aware that many tests require certain local data to be set up beforehand. As such, these tests can't really be run at a local site. As part of relocating our tools to the tool shed, we hope to fix this issue. Thanks, --nate On Feb 20, 2012, at 1:25 PM, Anne Pajon wrote: Hello, I am trying to have all functional tests on our production server (galaxy-dist 6621:26920e20157f) run successfully but I do still have failures that I do not know how to solve. Theses failures are related to unexpected differences probably due to versions of software that have been upgraded recently. ( Extract genomic DNA 1 ) Test-1 ( Extract genomic DNA 1 ) Test-2 ( Extract genomic DNA 1 ) Test-3 ( Extract genomic DNA 1 ) Test-4 ( Extract genomic DNA 1 ) Test-5 ( GeneBed_Maf_Fasta2 ) Test-1 ( Interval2Maf1 ) Test-1 ( Interval2Maf1 ) Test-3 ( Interval_Maf_Merged_Fasta2 ) Test-1 ( Interval_Maf_Merged_Fasta2 ) Test-2 ( LinearRegression1 ) Test-1 ( XY_Plot_1 ) Test-1 ( cca1 ) Test-1 ( histogram_rpy ) Test-1 ( kpca1 ) Test-1 ( pca1 ) Test-1 ( pca1 ) Test-2 ( pca1 ) Test-3 ( plot_for_lda_output1 ) Test-1 ( qual_stats_boxplot ) Test-1 AssertionError: History item 2 different than expected, difference (using diff) ( gops_join_1 ) Test-4 TwillAssertionError: code is 500 != 200 I do also have failures due to missing data but I am struggling to find out where to download them. ( gd_select_snps ) Test-1 AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error 'bighorn' does not appear in location file '/opt/local/home/webapp/galaxy/tool-data/gd.chrlens.loc' ( Annotation_Profiler_0 ) Test-1 ( Annotation_Profiler_0 ) Test-2 AssertionError: Configuration error: Table directory is missing (/opt/local/home/webapp/galaxy/tool-data/annotation_profiler/hg18) ( Interval2Maf_pairwise1 ) Test-1 AssertionError: Attempting to set field 'mafType' to value '['PAIRWISE_hg17_fr1']' in form 'tool_form' threw exception: cannot find value/label PAIRWISE_hg17_fr1 in list control ( maf_stats1 ) Test-1 ( maf_stats1 ) Test-2 AssertionError: Attempting to set field 'maf_source_type|mafType' to value '['8_WAY_MULTIZ_hg17']' in form 'tool_form' threw exception: cannot find value/label 8_WAY_MULTIZ_hg17 in list control ( phastOdds_for_intervals ) Test-1 AssertionError: Attempting to set field 'score_file' to value '['/galaxy/data/phastOdds_precomputed/encode_SEP-2005_\ tba.v2_phastOdds']' in form 'tool_form' threw exception: cannot find value/label /galaxy/data/phas..2_phastOdds in li\ st control ( aggregate_scores_in_intervals2 ) Test-1 ( aggregate_scores_in_intervals2 ) Test-2 AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error ( gencode_partition1 ) Test-1 Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error Error loading partitioning dataset. ( lda_analy1 ) Test-1 AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error The last failure is related to genome diversity and the fact that it calls python2.5. I've changed it to python for testing but the test still fails. ( gd_extract_flanking_dna ) Test-1 ( gd_extract_primers ) Test-1 ( gd_select_restriction_enzymes ) Test-1 AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error python2.5: command not found if changed to python: ERROR: 'NoneType' object has no attribute 'rfind' Is there a way to fix these failures? Any help would be very much appreciated. Thanks, Anne. -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)1223 404 334 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ 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: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by
[galaxy-dev] Sample tracking data transfer hangs in queue forever
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The galaxy_listener.log shows:
2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py
data_transfer
galaxy_hostrd-galaxydev.app.pmi/galaxy_host
api_key69bbd1a9b18eda2a888e9963820d8ef0/api_key
data_hostchp723/data_host
data_usergalaxy/data_user
data_passwordmypassword/data_password
request_id12/request_id
sample_id12/sample_id
library_id15/library_id
folder_id52/folder_iddataset
dataset_id10/dataset_id
namettt_2.fastq.gz/name
file/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz/file
/datasetdataset
dataset_id9/dataset_id
namettt_1.fastq.gz/name
file/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz/file
/dataset/data_transfer
universe_wsgi.ini
The FASTQ files are for testing and aren't very big (7.6 MB), what
could be going wrong?
regards,
Leandro
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Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever
I've got the same problem and when I looked at the data_transfer.log, I saw
the following message:
2012-03-01 15:12:27,338 - datatx_13870 -
(u'9c17d84742cd2acb63d88b5bd41d968f', u'
http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
{'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-01 15:12:27,342 - datatx_13870 - Error. !DOCTYPE HTML PUBLIC
-//IETF//DTD HTML 2.0//EN
htmlhead
title405 Method Not Allowed/title
/headbody
h1Method Not Allowed/h1
pThe requested method PUT is not allowed for the URL
/api/samples/2d9035b3fc152403./p
hr
Using Galaxy instead of Apache as the web server changed the sample status
from in queue to complete but didn't add the downloaded files to the data
library.
Luobin
On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida soft...@leandrohermida.com
wrote:
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The galaxy_listener.log shows:
2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py
data_transfer
galaxy_hostrd-galaxydev.app.pmi/galaxy_host
api_key69bbd1a9b18eda2a888e9963820d8ef0/api_key
data_hostchp723/data_host
data_usergalaxy/data_user
data_passwordmypassword/data_password
request_id12/request_id
sample_id12/sample_id
library_id15/library_id
folder_id52/folder_iddataset
dataset_id10/dataset_id
namettt_2.fastq.gz/name
file/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz/file
/datasetdataset
dataset_id9/dataset_id
namettt_1.fastq.gz/name
file/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz/file
/dataset/data_transfer
universe_wsgi.ini
The FASTQ files are for testing and aren't very big (7.6 MB), what
could be going wrong?
regards,
Leandro
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[galaxy-dev] database engine pool size
I would like to get some idea about 'database_engine_option_pool_size' and
'database_engine_option_max_overflow' settings. We seem to hit both of these
limits whenever a user runs a large workflow with following error:
{{{
TimeoutError: QueuePool limit of size 40 overflow 50 reached, connection timed
out, timeout 30
}}}
These limits are not reached for regular (non-workflow) galaxy jobs. Any help
on optimum values for these settings or performance tuning for workflow runs
would be appreciated.
Version Info: CentOS 5.7, PostgreSQL 8.4.9, Python 2.6.6, Galaxy revision
26920e20157f.
--
Thanks,
Shantanu
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Re: [galaxy-dev] Normal that latest galaxy-dist creates shed_tools directory one level up from the galaxy-dist directory?
Hi Leandro, The directory should not have been created upon Galaxy server start-up. This issue has been resolved in change set 6892:6b8535e5b030 in our central repository. Thanks for reporting this. Greg Von Kuster On Mar 26, 2012, at 5:57 AM, Leandro Hermida wrote: Dear all, Is it normal that the latest galaxy-dist creates a shed_tools directory one directory up (and outside) from the server galaxy-dist directory? best, Leandro ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] R scripts for DESeq
Hi Carlos,
Currently I am in a transition period, and I didn't get much time to look
on the same, Sorry for the delay.
For getting the read count, we wrote script and which is wrapped in Deseq
main program.
regards,
--Vipin T S
On 26 March 2012 14:01, Carlos Borroto carlos.borr...@gmail.com wrote:
Hi Vipin,
I was wondering if there is any progress on getting your DESeq wrapper
into the Tool Shed? I'm also highly interested on using DESeq inside
Galaxy.
Also, what you use for generating the read counts for DESeq? Do you
produce these counts inside Galaxy?
Thanks,
Carlos
On Thu, Feb 23, 2012 at 4:46 AM, Vipin TS vipin...@gmail.com wrote:
Hi Chris,
We are running DESEQ_VERSION 1.6.0 at our instance
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
thanks,
--Vipin T S
Which version of DESeq does this tool use?
Note that there are significant differences between DESeq 1.4 (the
version
described in the paper) and 1.6.x (current release). The differences are
both in functionality and results.
Regards,
Chris
On 23/02/2012 02:27, Greg Von Kuster g...@bx.psu.edu wrote:
Lisa,
In case you aren't aware, you can set your user preferences for your
account in the tool shed to receive an email message when a new
repository's first upload occurs. This would keep you from having to
check the tool shed. Go to User - Preferences - Manage
your email alerts and you'll see the following setting.
On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote:
Hi Vipin,
That is a wonderful news and I am eager to see it in tool shed. I am
going to check tool shed frequently these days to get it asap.
Thanks
Lisa
On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS vipin...@gmail.com
wrote:
Hi,
We have the recent release version of DESeq at our Galaxy instance,
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
I will add the Galaxy wrapper for DESeq in community tool shed in
few
days.
regards,
--Vipin
Hi Lisa,
I am going to send your question over to the galaxy-...@bx.psu.edu
mailing
list so that the development community can offer feedback.
http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clou
d_instance.2C_or_development_thread
http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clo
ud_instance.2C_or_development_thread
Th galaxy-user list is primarily for tool/data usage on the Galaxy
public
server.
http://wiki.g2.bx.psu.edu/Mailing%20Lists
Thanks,
Jen
Galaxy team
Original Message
Subject: [galaxy-user] R scripts for DESeq
Date: Tue, 21 Feb 2012 23:25:35 -0500
From: Liusong Yang liusongyang2...@gmail.com
To: galaxy-u...@lists.bx.psu.edu
Hello,
I am planning to put DESeq into galaxy. I am a newcomer for both
Galaxy and R. I have already read all of the related discussion in
this group. I also noticed that there are r_wrapper.sh and
DESeq.xml
added into galaxy recently under the path of tools.
These lines are from r_wrapper.sh.
### Run R providing the R script in $1 as standard input and
passing
### the remaining arguments on the command line
I guess this means we need to give the DESeq R script to the
wrapper
as standard input. My question is where or what is the DESeq R
scripts? I installed R and DESeq package, but I can not fund
anything
like DESeq.R or something similar? I feel so confusing now. Any
comments or suggestions would be absolutely appreciated!
Thanks
Lisa
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Re: [galaxy-dev] R scripts for DESeq
Thanks for the update.
I wonder if when you had the time to upload your script to the
toolshed, you could use a different name from just plain DESeq to
avoid confusion. A researcher might expect a DESeq tool to use a read
count table and not BAM files as input.
Kind regards,
Carlos
On Mon, Mar 26, 2012 at 2:49 PM, Vipin TS vipin...@gmail.com wrote:
Hi Carlos,
Currently I am in a transition period, and I didn't get much time to look on
the same, Sorry for the delay.
For getting the read count, we wrote script and which is wrapped in Deseq
main program.
regards,
--Vipin T S
On 26 March 2012 14:01, Carlos Borroto carlos.borr...@gmail.com wrote:
Hi Vipin,
I was wondering if there is any progress on getting your DESeq wrapper
into the Tool Shed? I'm also highly interested on using DESeq inside
Galaxy.
Also, what you use for generating the read counts for DESeq? Do you
produce these counts inside Galaxy?
Thanks,
Carlos
On Thu, Feb 23, 2012 at 4:46 AM, Vipin TS vipin...@gmail.com wrote:
Hi Chris,
We are running DESEQ_VERSION 1.6.0 at our instance
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
thanks,
--Vipin T S
Which version of DESeq does this tool use?
Note that there are significant differences between DESeq 1.4 (the
version
described in the paper) and 1.6.x (current release). The differences
are
both in functionality and results.
Regards,
Chris
On 23/02/2012 02:27, Greg Von Kuster g...@bx.psu.edu wrote:
Lisa,
In case you aren't aware, you can set your user preferences for your
account in the tool shed to receive an email message when a new
repository's first upload occurs. This would keep you from having to
check the tool shed. Go to User - Preferences - Manage
your email alerts and you'll see the following setting.
On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote:
Hi Vipin,
That is a wonderful news and I am eager to see it in tool shed. I am
going to check tool shed frequently these days to get it asap.
Thanks
Lisa
On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS vipin...@gmail.com
wrote:
Hi,
We have the recent release version of DESeq at our Galaxy instance,
http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq
I will add the Galaxy wrapper for DESeq in community tool shed in
few
days.
regards,
--Vipin
Hi Lisa,
I am going to send your question over to the galaxy-...@bx.psu.edu
mailing
list so that the development community can offer feedback.
http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clou
d_instance.2C_or_development_thread
http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clo
ud_instance.2C_or_development_thread
Th galaxy-user list is primarily for tool/data usage on the Galaxy
public
server.
http://wiki.g2.bx.psu.edu/Mailing%20Lists
Thanks,
Jen
Galaxy team
Original Message
Subject: [galaxy-user] R scripts for DESeq
Date: Tue, 21 Feb 2012 23:25:35 -0500
From: Liusong Yang liusongyang2...@gmail.com
To: galaxy-u...@lists.bx.psu.edu
Hello,
I am planning to put DESeq into galaxy. I am a newcomer for both
Galaxy and R. I have already read all of the related discussion in
this group. I also noticed that there are r_wrapper.sh and
DESeq.xml
added into galaxy recently under the path of tools.
These lines are from r_wrapper.sh.
### Run R providing the R script in $1 as standard input and
passing
### the remaining arguments on the command line
I guess this means we need to give the DESeq R script to the
wrapper
as standard input. My question is where or what is the DESeq R
scripts? I installed R and DESeq package, but I can not fund
anything
like DESeq.R or something similar? I feel so confusing now. Any
comments or suggestions would be absolutely appreciated!
Thanks
Lisa
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Please
Re: [galaxy-dev] [galaxy-user] Cleanup script error - guess_dialect_for_url
Hi Rocco,
To help us get oriented, which galaxy-dist pull did you start from and
which did you update to? If you have the release date/hg pull numbers,
that would be great. If you need to reference, these are the prior
distributions:
http://wiki.g2.bx.psu.edu/DevNewsBriefs
Ideally, you would be current through the March 12, 2012 distribution,
which included some bugs fixes for python 2.5 support. Support for
python 2.4 ended with the Nov 18, 2011 distribution.
If there is anything else customized about your system that you feel
would be relevant (other odd behavior?), that would be good to send
back. For example, can you delete and purge datasets through the UI?
Histories?
I am going to move your question over the galaxy-...@bx.psu.edu mailing
list, which is the best place to reach the development community. The
galaxy-user list is intended for data/tool usage questions, with a focus
on Galaxy main.
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
Please leave the galaxy-dev list in the cc for your return email,
Thanks!
Jen
Galaxy team
On 3/26/12 1:57 AM, rocco.piazza wrote:
Hello,
I'm working on a local instance of Galaxy-dist and I just
updated it. Right after the update I tried to run the
cleanup scripts. Unfortunately what I'm getting is the
following error:
# sh delete_datasets.sh -d 0 -r
Traceback (most recent call last):
File ./scripts/cleanup_datasets/cleanup_datasets.py,
line 524, in module
if __name__ == __main__: main()
File ./scripts/cleanup_datasets/cleanup_datasets.py,
line 101, in main
app = CleanupDatasetsApplication( config )
File ./scripts/cleanup_datasets/cleanup_datasets.py,
line 512, in __init__
self.model = galaxy.model.mapping.init(
config.file_path, config.database_connection,
engine_options={}, create_tables=False,
object_store=self.object_store )
File
/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py,
line 1818, in init
load_egg_for_url( url )
File
/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py,
line 1798, in load_egg_for_url
dialect = guess_dialect_for_url( url )
File
/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py,
line 1794, in guess_dialect_for_url
return (url.split(':', 1))[0]
AttributeError: 'bool' object has no attribute 'split'
The same error occurs if I try to run other cleanup
scripts, such as the delete_datasets or purge_datasets.
Any idea to solve this issue?
Best regards,
Rocco
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