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August 2012
- 95 participants
- 171 discussions
Hello,
Can you tell me how to become an 'admin' user on Galaxy, or else change the current admin?
Thank you.
-Ken.
2
1
On 08/24/2012 06:59 PM, kauerbach(a)comcast.net wrote:
> That's very helpful. Thank you. I'm new to Galaxy. Can you tell me how
> to become an 'admin' user and/or change the current admin user?
>
again, change the settings in "universe_wsgi.ini" by adding your e-mail
(the one you use to log into Galaxy):
#admin_users = foo(a)bar.com
Regards, Hans
> Thank you.
>
> -Ken.
>
> ------------------------------------------------------------------------
>
> *From: *"Hans-Rudolf Hotz" <hrh(a)fmi.ch>
> *To: *kauerbach(a)comcast.net
> *Cc: *galaxy-dev(a)lists.bx.psu.edu
> *Sent: *Friday, August 24, 2012 12:39:07 PM
> *Subject: *Re: [galaxy-dev] How to speed up job execution
>
>
>
> On 08/24/2012 05:22 PM, kauerbach(a)comcast.net wrote:
> > Hello,
> >
> > On our local instance of Galaxy jobs are taking an extremely long time
> > to run, or they are not run at all. In the history it always says "job
> > is waiting to run", even simple jobs like reformatting text files to be
> > tab delimited. Is there a way to 1) check the Galaxy job queue, and 2)
> > perhaps modify some parameters to speed up processing?
> >
> > Any suggestions would be greatly appreciated.
> >
>
> Hi Kenneth
>
> Usually, Galaxy is not slow, but the tools executed by Galaxy are slow
> (eg due to bad IO performance of the host server).
>
> "job is waiting to run" indicates there are unfinished jobs in the
> queue. There are two ways to check the queue:
>
> If you are an 'Admin', select the Admin tab -> "Manage jobs". This will
> list all running jobs. And you can kill jobs as well.
>
> Or use the galaxy report tools and have a look at "Today's jobs"
>
>
>
> Depending on your set-up, you might consider changing "universe_wsgi.ini":
>
> # Number of concurrent jobs to run (local job runner)
> local_job_queue_workers = 5
>
> to allow more parallel jobs
>
>
>
> Hope this helps
> Hans
>
>
>
> > Thank you.
> >
> >
> >
> >
> > ___________________________________________________________
> > 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/
> >
>
1
0
Hello,
On our local instance of Galaxy jobs are taking an extremely long time to run, or they are not run at all. In the history it always says "job is waiting to run", even simple jobs like reformatting text files to be tab delimited. Is there a way to 1) check the Galaxy job queue, and 2) perhaps modify some parameters to speed up processing?
Any suggestions would be greatly appreciated.
Thank you.
2
1
Hi Team,
I am attempting to get the reports interface for my galaxy server to function. I have my reports.wsgi.ini configured so:
# ---- HTTP Server ----------------------------------------------------------
[server:main]
use = egg:Paste#http
port = 9001
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10
# ---- Galaxy Webapps Report Interface -------------------------------------------------
[app:main]
# Specifies the factory for the universe WSGI application
paste.app_factory = galaxy.webapps.reports.buildapp:app_factory
log_level = DEBUG
# Database connection
# Galaxy reports are intended for production Galaxy instances, so sqlite is not supported.
# You may use a SQLAlchemy connection string to specify an external database.
database_connection = postgres:///galaxy_1
# Where dataset files are saved
file_path = database/files
# Temporary storage for additional datasets, this should be shared through the cluster
new_file_path = database/tmp
# Session support (beaker)
use_beaker_session = True
session_type = memory
session_data_dir = %(here)s/database/beaker_sessions
session_key = galaxysessions
session_secret = changethisinproduction
# Configuration for debugging middleware
# debug = true
use_lint = false
# NEVER enable this on a public site (even test or QA)
# use_interactive = true
# path to sendmail
# sendmail_path = /usr/sbin/sendmail
# Address to join mailing list
# mailing_join_addr = galaxy-user-join(a)bx.psu.edu<mailto:galaxy-user-join@bx.psu.edu>
# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!)
## use_heartbeat = True
# Profiling middleware (cProfile based)
## use_profile = True
# Mail
smtp_server = smtp.jax.org
error_email_to = cbr-help(a)jax.org<mailto:cbr-help@jax.org>
# Use the new iframe / javascript based layout
use_new_layout = true
# Serving static files (needed if running standalone)
static_enabled = True
static_cache_time = 360
static_dir = %(here)s/static/
static_images_dir = %(here)s/static/images
static_favicon_dir = %(here)s/static/favicon.ico
static_scripts_dir = %(here)s/static/scripts/
static_style_dir = %(here)s/static/june_2007_style/blue
The reports_webapp.log shows no errors but the process never completes loading. I stop the process manually after 20 minutes or more and no reports interface:
python path is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages
galaxy.model.custom_types DEBUG 2012-08-20 13:03:04,572 psycopg2 egg successfully loaded for postgres dialect
galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,297 Enabling 'users' controller, class: Users
galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,310 Enabling 'system' controller, class: System
galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,354 Enabling 'sample_tracking' controller, class: SampleTracking
galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,379 Enabling 'jobs' controller, class: Jobs
galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,418 Enabling 'workflows' controller, class: Workflows
galaxy.web.framework.base DEBUG 2012-08-20 13:03:09,430 Enabling 'root' controller, class: Report
galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,433 Enabling 'httpexceptions' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,443 Enabling 'recursive' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,590 Enabling 'error' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,601 Enabling 'trans logger' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,601 Enabling 'config' middleware
galaxy.webapps.reports.buildapp DEBUG 2012-08-20 13:03:09,614 Enabling 'x-forwarded-host' middleware
Starting server in PID 15823.
serving on http://127.0.0.1:9001
Removing PID file reports_webapp.pid
I am not sure what is going on, but I need to get this working again. Any help would be greatly appreciated.
Thanks,
Iry
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2
2
Anyone developing API scripts who likes to live dangerously - please read
on.
I just tested and blend-lib api scripts work fine in Galaxy when pasted
into a Tool Factory form. No need to generate a new tool.
Compared with running in a console, you get persistence and other framework
benefits plus at no extra charge, a ginormous security problem if you share
the history or any outputs because they contain the api script with key so
development servers only please!
Leave the input box empty, set the interpreter to python, paste and run an
api script - eg working example (substitute the url and key) below.
Took me a few iterations to develop the example - after each run, the
(edited..) api script is conveniently recreated using the redo button on
the history output item.
So each successive version of the developing api script I ran was persisted
- ready to be edited and rerun easily - handy being able to quickly inspect
dicts to help move progressively deeper iteratively.
Give the below a whirl on a private clone (install the tool factory from
the main toolshed) and try adding complexity with few rerun/edit/rerun
cycles.
=============Eg tool factory api script=======================
import sys
from blend.galaxy import GalaxyInstance
ourGal = 'http://x.x.x.x:xxxx'
ourKey = 'xxx'
gi = GalaxyInstance(ourGal, key=ourKey)
libs = gi.libraries.get_libraries()
res = []
for lib in libs: #u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id':
u'441d8112651dc2f3', u'name': u'Demonstration sample RNA data',
res.append('%s:\n' % lib['name'])
res.append(str(gi.libraries.show_library(lib['id'],contents=True)))
outf=open(sys.argv[2],'w')
outf.write('\n'.join(res))
outf.close()
returns a history item with:
Demonstration sample RNA data:[{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/F8de0c7750d06c0d0',
u'type': u'folder', u'name': u'/', u'id': u'F8de0c7750d06c0d0'}, {u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/F7d480bbb847db8d0',
u'type': u'folder', u'name': u'/rnaseq demo data', u'id':
u'F7d480bbb847db8d0'}, {u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/8b25a086f3d48921',
u'type': u'file', u'name': u'/rnaseq demo
data/hg19_exons_mergedGENENAMES.bed', u'id': u'8b25a086f3d48921'}, {u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/5091b660e3557a3e',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
Ctrl_HAEC_FC078_1_sequence.txt (data 1)', u'id': u'5091b660e3557a3e'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/4e084a2837e50c40',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
Ctrl_HAEC_FC078_4_sequence.txt (data 4)', u'id': u'4e084a2837e50c40'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/0ab9ae3dbe24ad04',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
Ctrl_HAEC_FC079_1_sequence.txt (data 7)', u'id': u'0ab9ae3dbe24ad04'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/0a773730795f59a9',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HG_HAEC_FC078_2_sequence.txt (data 2)', u'id': u'0a773730795f59a9'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/c810c4dc5aed60ac',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HG_HAEC_FC078_5_sequence.txt (data 5)', u'id': u'c810c4dc5aed60ac'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/ee5b8d53fd29c05c',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HG_HAEC_FC079_2_sequence.txt (data 8)', u'id': u'ee5b8d53fd29c05c'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/1e04e5f52ca2af6e',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HN_HAEC_FC078_3_sequence.txt (data 3)', u'id': u'1e04e5f52ca2af6e'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/7e05ba393ab04bc6',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HN_HAEC_FC078_6_sequence.txt (data 6)', u'id': u'7e05ba393ab04bc6'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/335753abc7341224',
u'type': u'file', u'name': u'/rnaseq demo data/Select first on
HN_HAEC_FC079_3_sequence.txt (data 9)', u'id': u'335753abc7341224'},
{u'url':
u'/galaxy/api/libraries/441d8112651dc2f3/contents/09c975479974360d',
u'type': u'file', u'name': u'/smalltest.sam', u'id':
u'09c975479974360d'}]Public
data:[{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F37c082b4cb3811bd',
u'type': u'folder', u'name': u'/', u'id': u'F37c082b4cb3811bd'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F5390d290c0aca35b',
u'type': u'folder', u'name': u'/1000 genomes and other public fastq and bam
samples', u'id': u'F5390d290c0aca35b'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/721cc53ac555050e',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq',
u'id': u'721cc53ac555050e'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/a96ce863d2b9a69a',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq(data
10)_FastQC.html', u'id': u'a96ce863d2b9a69a'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/81d4a112e7668435',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/1000g paired sample chr20', u'id': u'81d4a112e7668435'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/00776454b8f394c8',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/1000g chrom 10 single QC sample', u'id': u'00776454b8f394c8'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/0ff2a12d5b5e045a',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/1000g sample chr1 single ended reads', u'id': u'0ff2a12d5b5e045a'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/8b394966390e7e29',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/Galaxy_GM12878.fastqillumina', u'id': u'8b394966390e7e29'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/1b82079d07b4928f',
u'type': u'file', u'name': u'/1000 genomes and other public fastq and bam
samples/Galaxy_GM12878.fastqilluminaFastQC.html', u'id':
u'1b82079d07b4928f'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F2ef8c0af274c514d',
u'type': u'folder', u'name': u'/BioMart', u'id': u'F2ef8c0af274c514d'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F1ba8da1da6710cd5',
u'type': u'folder', u'name': u'/BioMart/RefSeq2GeneName', u'id':
u'F1ba8da1da6710cd5'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/b5e989c148cd0aa1',
u'type': u'file', u'name':
u'/BioMart/RefSeq2GeneName/mm9_Names_RefSeq.txt', u'id':
u'b5e989c148cd0aa1'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F6cd82b8eed63ee9a',
u'type': u'folder', u'name': u'/encode', u'id': u'F6cd82b8eed63ee9a'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F177c1b293cbb701a',
u'type': u'folder', u'name': u'/encode/FAIRE', u'id':
u'F177c1b293cbb701a'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/ee24d81f0dee6a46',
u'type': u'file', u'name': u'/encode/FAIRE/FASTQ Groomer on data 1', u'id':
u'ee24d81f0dee6a46'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/f4209c75ea186d52',
u'type': u'file', u'name':
u'/encode/FAIRE/wgEncodeUncFAIREseqRawDataRep2K562.fastq', u'id':
u'f4209c75ea186d52'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/cca5cab06be4a64c',
u'type': u'file', u'name':
u'/encode/FAIRE/wgEncodeUncFAIREseqRawDataRep2K562.fastq', u'id':
u'cca5cab06be4a64c'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/Fa72f7b1e35fa5a2e',
u'type': u'folder', u'name': u'/EpiDfiles', u'id': u'Fa72f7b1e35fa5a2e'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/fa29d7e45271edc8',
u'type': u'file', u'name': u'/EpiDfiles/c2.all.v2.5.symbols.gmt', u'id':
u'fa29d7e45271edc8'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/42a6cd9d5e1f6e99',
u'type': u'file', u'name': u'/EpiDfiles/hg18_refSeq_HUGO_TSS.bed', u'id':
u'42a6cd9d5e1f6e99'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/5d3a4056a308beac',
u'type': u'file', u'name': u'/EpiDfiles/msigdb.v2.5.symbols.gmt', u'id':
u'5d3a4056a308beac'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/02f72b1bb3982091',
u'type': u'file', u'name': u'/EpiDfiles/msigdb.v3.0.symbols.gmt', u'id':
u'02f72b1bb3982091'}, {u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/F1bae78f62566eb60',
u'type': u'folder', u'name': u'/hg18', u'id': u'F1bae78f62566eb60'},
{u'url':
u'/galaxy/api/libraries/37c082b4cb3811bd/contents/d6f2ea9a5a8e9773',
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validation/FC095_2_BC11_GGCTAC_split_trimmed.txt', u'id':
u'010a58f18c61f217'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/43af962da532299f',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_2_BC12_CTTGTA_split_trimmed.txt', u'id':
u'43af962da532299f'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/877ddb236fe3c89d',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_2_unmatched_split_trimmed.txt', u'id':
u'877ddb236fe3c89d'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/af006d8e64e69e55',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC01_ATCACG_split_trimmed.txt', u'id':
u'af006d8e64e69e55'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/c087711466d2d6d7',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC02_CGATGT_split_trimmed.txt', u'id':
u'c087711466d2d6d7'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/f07ea4c6512d723a',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC03_TTAGGC_split_trimmed.txt', u'id':
u'f07ea4c6512d723a'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/017407ed673f0be2',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC04_TGACCA_split_trimmed.txt', u'id':
u'017407ed673f0be2'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/67957017724be4d0',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC05_ACAGTG_split_trimmed.txt', u'id':
u'67957017724be4d0'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/d12315e895b73e45',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC06_GCCAAT_split_trimmed.txt', u'id':
u'd12315e895b73e45'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/9aa7dd3be645f98e',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC07_CAGATC_split_trimmed.txt', u'id':
u'9aa7dd3be645f98e'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/0148b475f0c40eff',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC08_ACTTGA_split_trimmed.txt', u'id':
u'0148b475f0c40eff'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/7c0f690c9fa27398',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC09_GATCAG_split_trimmed.txt', u'id':
u'7c0f690c9fa27398'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/8bc34a1495a5a647',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC10_TAGCTT_split_trimmed.txt', u'id':
u'8bc34a1495a5a647'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/33c408a265004f2b',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC11_GGCTAC_split_trimmed.txt', u'id':
u'33c408a265004f2b'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/5e427c83d16d17e2',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_BC12_CTTGTA_split_trimmed.txt', u'id':
u'5e427c83d16d17e2'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/7960b6ec99001c86',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_3_unmatched_split_trimmed.txt', u'id':
u'7960b6ec99001c86'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/5399da4419f4718c',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC01_ATCACG_split_trimmed.txt', u'id':
u'5399da4419f4718c'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/e42f89121cf7d56c',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC02_CGATGT_split_trimmed.txt', u'id':
u'e42f89121cf7d56c'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/d3d80b3138f7c057',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC03_TTAGGC_split_trimmed.txt', u'id':
u'd3d80b3138f7c057'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/29c33cd3eed7b56b',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC04_TGACCA_split_trimmed.txt', u'id':
u'29c33cd3eed7b56b'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/a342c2ae1156cd5f',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC05_ACAGTG_split_trimmed.txt', u'id':
u'a342c2ae1156cd5f'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/200bd26280687978',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC06_GCCAAT_split_trimmed.txt', u'id':
u'200bd26280687978'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/5067ac18fed90ea6',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC07_CAGATC_split_trimmed.txt', u'id':
u'5067ac18fed90ea6'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/cf52fe9f95fc91ef',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC08_ACTTGA_split_trimmed.txt', u'id':
u'cf52fe9f95fc91ef'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/1edcd7aa2bf7ea43',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC09_GATCAG_split_trimmed.txt', u'id':
u'1edcd7aa2bf7ea43'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/cef69438f673a7b4',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC10_TAGCTT_split_trimmed.txt', u'id':
u'cef69438f673a7b4'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/a0f74b626cb27c2a',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC11_GGCTAC_split_trimmed.txt', u'id':
u'a0f74b626cb27c2a'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/8dfbcdc4d91895aa',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_BC12_CTTGTA_split_trimmed.txt', u'id':
u'8dfbcdc4d91895aa'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/05864379043148a3',
u'type': u'file', u'name': u'/Truseq microRNA
validation/FC095_4_unmatched_split_trimmed.txt', u'id':
u'05864379043148a3'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/Fec775317423c30f0',
u'type': u'folder', u'name': u'/TSA', u'id': u'Fec775317423c30f0'},
{u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/f00a75e5b7ebee79',
u'type': u'file', u'name': u'/TSA/FC039_1_Hg19.bam', u'id':
u'f00a75e5b7ebee79'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/9591f638cc99f66f',
u'type': u'file', u'name':
u'/TSA/H3K4Me3_from_control_Rep1_FC046_6_Hg19.bam', u'id':
u'9591f638cc99f66f'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/e93ce88dbaca4d2e',
u'type': u'file', u'name':
u'/TSA/H3K4Me3_from_control_Rep2_FC047_3_Hg19.bam', u'id':
u'e93ce88dbaca4d2e'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/367619ade287d0d5',
u'type': u'file', u'name':
u'/TSA/H3K4Me3_from_control_Rep3_FC049_3_Hg19.bam', u'id':
u'367619ade287d0d5'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/deed45e777c7e5d0',
u'type': u'file', u'name': u'/TSA/H3K4Me3_from_TSA_Rep1_FC046_4_Hg19.bam',
u'id': u'deed45e777c7e5d0'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/45fc2e8bc798825b',
u'type': u'file', u'name': u'/TSA/H3K4Me3_from_TSA_Rep2_FC047_5_Hg19.bam',
u'id': u'45fc2e8bc798825b'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/7183f39ae3a380e5',
u'type': u'file', u'name': u'/TSA/H3K4Me3_from_TSA_Rep3_FC049_5_Hg19.bam',
u'id': u'7183f39ae3a380e5'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/1241cf2b6ac79906',
u'type': u'file', u'name': u'/TSA/H3K9K14ac_control_Rep1_FC041_6_Hg19.bam',
u'id': u'1241cf2b6ac79906'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/4064748ece9ea595',
u'type': u'file', u'name': u'/TSA/H3K9K14ac_control_Rep2_FC039_2_Hg19.bam',
u'id': u'4064748ece9ea595'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/bf5903809888f264',
u'type': u'file', u'name': u'/TSA/H3K9K14ac_control_Rep3_FC039_5_Hg19.bam',
u'id': u'bf5903809888f264'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/90fc2461c447ec29',
u'type': u'file', u'name': u'/TSA/H3K9K14ac_TSA_Rep1_FC041_8_Hg19.bam',
u'id': u'90fc2461c447ec29'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/ce78c44e48ce8a17',
u'type': u'file', u'name': u'/TSA/H3K9K14ac_TSA_Rep2_FC039_4_Hg19.bam',
u'id': u'ce78c44e48ce8a17'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/5e65073893ec2b34',
u'type': u'file', u'name': u'/TSA/H3K9K14ac_TSA_Rep3_FC039_7_Hg19.bam',
u'id': u'5e65073893ec2b34'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/4be747faf5c6c903',
u'type': u'file', u'name':
u'/TSA/H3K9Me3_from_control_Rep1_FC046_3_Hg19.bam', u'id':
u'4be747faf5c6c903'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/bf16841bdc9180b6',
u'type': u'file', u'name':
u'/TSA/H3K9Me3_from_control_Rep2_FC047_6_Hg19.bam', u'id':
u'bf16841bdc9180b6'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/f1604623ed2108b3',
u'type': u'file', u'name':
u'/TSA/H3K9Me3_from_control_Rep3_FC049_6_Hg19.bam', u'id':
u'f1604623ed2108b3'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/2f5b0f6a9a760ece',
u'type': u'file', u'name': u'/TSA/H3K9Me3_from_TSA_Rep1_FC046_1_Hg19.bam',
u'id': u'2f5b0f6a9a760ece'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/a82e6c0999aadeae',
u'type': u'file', u'name': u'/TSA/H3K9Me3_from_TSA_Rep2_FC047_8_Hg19.bam',
u'id': u'a82e6c0999aadeae'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/6699d921a10c85ee',
u'type': u'file', u'name': u'/TSA/H3K9Me3_from_TSA_Rep3_FC049_8_Hg19.bam',
u'id': u'6699d921a10c85ee'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/68157400817aa6ad',
u'type': u'file', u'name':
u'/TSA/Input_from_control_Rep1_FC046_8_Hg19.bam', u'id':
u'68157400817aa6ad'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/025f175e3b559f4d',
u'type': u'file', u'name':
u'/TSA/Input_from_control_Rep2_FC047_1_Hg19.bam', u'id':
u'025f175e3b559f4d'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/f9018830f759dc89',
u'type': u'file', u'name': u'/TSA/Input_from_TSA_Rep2_FC047_2_Hg19.bam',
u'id': u'f9018830f759dc89'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/6fc8f18f27e0a7fc',
u'type': u'file', u'name':
u'/kingwellRN4_all_june19_bams2mx.xls_bams2mx.xls', u'id':
u'6fc8f18f27e0a7fc'}, {u'url':
u'/galaxy/api/libraries/6cd82b8eed63ee9a/contents/6b99893c97b706d9',
u'type': u'file', u'name': u'/Reginald_IPS_cat_merged_peaks.mx', u'id':
u'6b99893c97b706d9'}]
1
0
patch for vcf QUAL field with missing value "." in lib/galaxy/visualization/tracks/data_providers.py
by Jim Johnson 23 Aug '12
by Jim Johnson 23 Aug '12
23 Aug '12
The VCF format ( http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-varian… )
specifies "." to represent missing values.
lib/galaxy/visualization/tracks/data_providers.py throws an float conversion error when the qual field of a vcf file has the missing value: "."
This can be remedied with the following patch, trackster handles the "None" value when displaying the variant.
diff -r eb542e228a0f lib/galaxy/visualization/tracks/data_providers.py
--- a/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:56:49 2012 -0500
+++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:58:46 2012 -0500
@@ -634,7 +634,7 @@
# TODO? VCF does not have strand, so default to positive.
"+",
new_seq,
- float( feature[5] ) ]
+ None if feature[5] == '.' else float( feature[5] ) ]
rval.append(payload)
return { 'data': rval, 'message': message }
2
1
Hi,
I would like to run a Java program that accepts a VCF file from Galaxy and uses a JDBC connection to a postgreSQL database to do some analysis. The program should procude an HTML table that is then displayed in the Galaxy browser window. We have a local Galaxy server, and I have added my program to it using a configuration file. When I start the program via the framework, it just hangs, and "runs" forever (the command line version finishes in a few seconds). I am relatively new to Galaxy and have not been able to find out how to trouble shoot this in the documentation.
Some questions:
1) The tables in the postgreSQL database have been set to GRANT SELECT TO PUBLIC, and the Java program is connecting to the database with the name and password of the owner of the database. Are there any other permissions issues that result from the Galaxy framework?
2) Is there some way of following program execution from a shell to see what Galaxy is doing?
3) Any other ideas?
thanks Peter
PD Dr. med. Peter N. Robinson, MSc.
Institut für Medizinische Genetik und Humangenetik
Charité - Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
peter.robinson(a)charite.de
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
1
0
Hi all,
I'm trying to run galaxy-central on my laptop in order to play around
with some changes, and I'm having trouble getting it to run. I can run
galaxy-dist without problems and have been working with that (so its
eggs are all installed already), but now I want to create a pull
request so want to run galaxy-dist. I'm not trying to install any
extra tools or data, just the code.
I'm running on OSX 10.7.4 and using virtualenv. I have Enthought
installed, and I assume I will be using its version of python by
default. The default python seems to be 2.7.3.
I'm using the same virtualenv environment for galaxy-dist and
galaxy-central (though it doesn't seem to matter if I give
galaxy-central its own environment, I see the same error). So the
steps were:
- create a virtualenv environment and activate it
- get galaxy-dist and call run.sh - it asked me to build quite a lot
of dependencies myself, which was just a matter of running the
requested commands, and then it worked with no problems.
- shut down galaxy-dist, and in another directory, get galaxy-central
and call run.sh. I think it asked me to build a couple of
dependencies, but then it gives up with the following:
(galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh --reload
Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing,
this is almost certainly a bug in the egg distribution.
Dependency "ssh" requires "pycrypto>=2.1,!=2.4"
Traceback (most recent call last):
File "./scripts/fetch_eggs.py", line 30, in <module>
c.resolve() # Only fetch eggs required by the config
File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py",
line 345, in resolve
egg.resolve()
File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py",
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File "/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (ssh 1.7.14
(/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg),
Requirement.parse('pycrypto>=2.1,!=2.4'))
Fetch failed.
Any idea what is causing this?
Thanks,
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357 M: 0414 854 759
4
8
Well.. it turned out to be pretty easy thanks to the efforts of Dannon and Brian Ondov
I've added the metaphlan2krona.py script to the metaphlan toolshed repo.
diff -r e88fa24fa837 metaphlan.xml
--- a/metaphlan.xml Wed Jun 06 10:41:23 2012 -0400
+++ b/metaphlan.xml Wed Aug 22 21:36:21 2012 -0400
@@ -14,7 +14,7 @@
</command>
<inputs>
- <param format="fasta" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param>
+ <param format="fasta,fastq,fastqsanger" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param>
<param name="PresetsForBowtie2" type="select" format="text">
<label>Sensitivity options for read-marker similarity (as described by BowTie2)</label>
<option value="very-sensitive-local">Very Sensitive Local</option>
diff -r e88fa24fa837 metaphlan2krona.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan2krona.py Wed Aug 22 21:36:21 2012 -0400
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+
+# ==============================================================================
+# Conversion script: from MetaPhlAn output to Krona text input file
+# Author: Daniel Brami (daniel.brami(a)gmail.com<mailto:daniel.brami@gmail.com>)
+# ==============================================================================
+
+import sys
+import optparse
+import re
+
+def main():
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ parser.add_option( '-p', '--profile', dest='profile', default='', action='store', help='The input file is the MetaPhlAn standard result file' )
+ parser.add_option( '-k', '--krona', dest='krona', default='krona.out', action='store', help='the Krons output file name' )
+ ( options, spillover ) = parser.parse_args()
+
+ if not options.profile or not options.krona:
+ parser.print_help()
+ sys.exit()
+
+ re_candidates = re.compile(r"s__|unclassified\t")
+ re_replace = re.compile(r"\w__")
+ re_bar = re.compile(r"\|")
+
+ metaPhLan = list()
+ with open(options.profile,'r') as f:
+ metaPhLan = f.readlines()
+ f.close()
+
+ krona_tmp = options.krona
+ metaPhLan_FH = open(krona_tmp, 'w')
+
+ for aline in (metaPhLan):
+ if(re.search(re_candidates, aline)):
+ x=re.sub(re_replace, '\t', aline)
+ x=re.sub(re_bar, '', x)
+
+ x_cells = x.split('\t')
+ lineage = '\t'.join(x_cells[0:(len(x_cells) -1)])
+ abundance = float(x_cells[-1].rstrip('\n'))
+
+ metaPhLan_FH.write('%s\n'%(str(abundance) + '\t' + lineage))
+
+ metaPhLan_FH.close()
+
+if __name__ == '__main__':
+ main()
diff -r e88fa24fa837 metaphlan_to_krona.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan_to_krona.xml Wed Aug 22 21:36:21 2012 -0400
@@ -0,0 +1,17 @@
+<tool id="meta_to_krona" name="MetaPhlAn to Krona" version="1.0.0">
+ <description>Converter</description>
+ <command interpreter="python">
+metaphlan2krona.py -p $input -k $output
+ </command>
+ <inputs>
+ <param name="input" type="data" format="tabular" label="Input MetaPhlAn File"/>
+ </inputs>
+ <outputs>
+ <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+ MetaPhlAn to Krona Converter
+ </help>
+</tool>
To get it to work with krona i extended the krona repo like this
diff -r 42c899125802 krona/krona.xml
--- a/krona/krona.xml Mon Mar 19 17:39:59 2012 -0400
+++ b/krona/krona.xml Wed Aug 22 21:39:17 2012 -0400
@@ -7,15 +7,18 @@
ktImportBLAST
-e ${type.factor}
${type.random}
+ #else if $type.program == 'krona':
+ ktImportText
#else
ktImportTaxonomy
${type.summary}
#end if
- -o $output
+ -o $output
${type.include}
+ #unless $type.program == 'krona'
+ -d $depth
+ #end unless
- -d $depth
-
## uncomment for isolated intranets (see README)
##
##-u /static/krona
@@ -36,6 +39,7 @@
<option value="galaxy">Galaxy taxonomic representation</option>
<option value="blast">Tabular BLAST results</option>
<option value="taxonomy">Taxonomy ID list</option>
+ <option value="krona">Krona format</option>
</param>
<when value="galaxy">
<param name="factor" type="hidden" value=""/>
@@ -51,6 +55,10 @@
<param name="summary" type="boolean" truevalue="-m 1" falsevalue="" label="Summarized" help="The first column is counts rather than query IDs."/>
<param name="include" type="boolean" truevalue="-i" falsevalue="" label="Include reads with no hits"/>
</when>
+ <when value="krona">
+ <param name="factor" type="hidden" value=""/>
+ <param name="include" type="hidden" value=""/>
+ </when>
</conditional>
<param name="depth" label="Depth" type="integer" help="The maximum depth to show in the chart (0 for unlimited)." value="0"/>
<conditional name="datasets">
now i see this kind of graph
[cid:D121407D-64B6-4D03-AE23-9DC53B52B5DC@home.langhorst.com]
one more item.. had to add
sanitize_all_html = False
to universe_wsgi.ini
brad
--
Brad Langhorst
langhorst(a)neb.com<mailto:langhorst@neb.com>
978-380-7564
1
0
I have installed both krona and metphlan from the toolshed to my local insttance.
both seem to work ok, but I don't seen an easy way to get the metaphlan output into a form that krona can accept.
has anybody solved this problem already?
Brad
--
Brad Langhorst
langhorst(a)neb.com<mailto:langhorst@neb.com>
978-380-7564
1
0