Adding the tag in tool xml file
by sshashi
Hi,
is it possible to add the tag in tool_xml_file ? how can i add new tag
in tool_xml_file ? if anyone is working on this , guide me ....
Regards
shashi
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10 years, 6 months
conflicting migration files
by Langhorst, Brad
When I merged brad chapmans code into galaxy-central two 0099 migration files are created.
I got things working by moving the ngs lims one to 0104 , but now i think i'll be in for a problem when a new 104 is created...
What's the right way to solve this?
Brad
--
Brad Langhorst
langhorst(a)neb.com<mailto:langhorst@neb.com>
978-380-7564
10 years, 6 months
Question about compressed files
by Ciara Ledero
Hi all,
My colleague tried to upload via filesystem path a file with an approximate
size of 2GB. It was a compressed file (filename.fq.gz). No error was
reported, so I thought everything went fine, but when he tried running a
tool, the uploaded file did not show in the input dropdown. But when he
tried again, this time using an uncompressed file, every thing worked well.
Now to my question: by default, can Galaxy accept and use compressed files?
Or do I have to change something in its configuration just to do so?
Thanks for the help!
CL
10 years, 6 months
Byte-range support for IGV ?
by Chebbi Mohamed Amine
HELLO !
I just updated our local galaxy instance and just wanted to try the new IGV
display application. When I try to display a BAM file whith the local IGV,
I encounter the following message :
"HTTP and FTP access to BAM files require byte-range support"
Has anyone encountred the same probleme?
Thanks in advances
Regards
Amine
10 years, 6 months
how to add new Xml tag in tool xml file
by sshashi
Hi,
I am using my local instance of galaxy . I want to create a tag which
will open an new window in galaxy. How can i create a new tag in
tool_xml_file ? for this any modification is required in any file of
galaxy ?
Regards
shashi
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contain confidential and privileged information. If you are not the
intended recipient, please contact the sender by reply e-mail and destroy
all copies and the original message. Any unauthorized review, use,
disclosure, dissemination, forwarding, printing or copying of this email
is strictly prohibited and appropriate legal action will be taken.
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10 years, 6 months
how to create a new tag in tool_xml_file of galaxy
by sshashi
Hi,
I am using my local instance of galaxy . I want to create a tag which
will open an new window in galaxy. How can i create a new tag in
tool_xml_file ? for this any modification is required in any file of
galaxy ?
Regards
shashi
-------------------------------------------------------------------------------------------------------------------------------
This e-mail is for the sole use of the intended recipient(s) and may
contain confidential and privileged information. If you are not the
intended recipient, please contact the sender by reply e-mail and destroy
all copies and the original message. Any unauthorized review, use,
disclosure, dissemination, forwarding, printing or copying of this email
is strictly prohibited and appropriate legal action will be taken.
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10 years, 6 months
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
by Iry Witham
I am still experiencing issues getting my galaxy server to start since the upgrade. The logs are all getting this type of error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat runner0.log
python path is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-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/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages
galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg successfully loaded for postgres dialect
Traceback (most recent call last):
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self )
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py", line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '101' but this code expects version '97'. Please backup your database and then migrate the schema by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid
I have not dropped my database and built it fresh. However, I have attempted the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for both the runner and web app ini files with the following error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
File "./scripts/manage_db.py", line 63, in <module>
main( repository=repo, url=db_url )
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main
ret = command_func(**kwargs)
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 327, in _migrate
changeset = schema.changeset(version)
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 173, in changeset
changeset = self.repository.changeset(database, start_ver, version)
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py", line 170, in changeset
changes = [self.version(v).script(database, op) for v in versions]
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py", line 145, in version
return self.versions.version(*p, **k)
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/version.py", line 125, in version
return self.versions[VerNum(vernum)]
KeyError: <VerNum(101)>
Any suggestions?
Thanks,
Iry
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10 years, 7 months
bug in transferring files in Galaxy to the UCSC browser
by David Gilmour
Hi,
For some time now, we have found that wig files on the Penn State Galaxy cannot be transferred into the UCSC browser via the Galaxy URL. We receive the error: " Error Unrecognized format line 2 of https://main.g2.bx.psu.edu/datasets/329241/display/: (note: chrom names are case sensitive)". When we examine the file, the case is correct. Moreover, if we download the file and upload it to the UCSC browser directly from our computer, the data is properly displayed. A search of the Mailing List with the following phrase: "note: chrom names are case sensitive", brings up some discussion of this issue but I was unable to find a resolution.
Thanks
*********************************************
David S. Gilmour
Professor of Biochemistry and Molecular Biology
Center for Eukaryotic Gene Regulation
Department of Biochemistry and Molecular Biology
465A North Frear
Penn State University
University Park, PA 16802
Office: 814-863-8905
Lab: 814-865-3795
Fax: 814-863-7024
Cellphone: 814-777-4166
Research web page: http://bmb.psu.edu/directory/dsg11
BMB Department: http://bmb.psu.edu/
Center for Eukaryotic Gene Regulation: http://www.huck.psu.edu/institutes-and-centers/cgr
10 years, 7 months
how to add check-boxes and button in new page
by Neetu Ojha
Hello,
The first thing is absolutely new to the python.
I am trying to integrate data-grid with GALAXY to host the pubchem data.
For doing so I have created one .mako to add page and added one function in
user.py. it adds one button as shown in the attachment. on click of the
button it redirects to new page where the output is displayed as shown in
the image file galaxy-op.png in attachment.
My requirment is to have check boxes against the list of the files and add
one button upload in the page shown in the file attached galaxy-op.png,
which when clicked upload the data from the data-grid using some python
script to local point.
Kindly guide on that what to do.
The changes done so far i present down:
In the file /root/galaxy-dist/lib/galaxy/web/controllers/user.py
Added :
def gsrm_data( self, trans, webapp='galaxy'):
# session = trans.sa_session
# user = session.query( model.User ).filter_by( username=username
).first()
user = trans.get_user()
prxy="/root/x509up_u3163"
refresh_frames = [ 'masthead']
os.environ["X509_USER_PROXY"]=prxy
os.environ["PATH"]=os.environ["PATH"]+":/usr/local/GLOBUS-4.0.8/bin/:/usr/local/dpm/bin/:/usr/local/glite/bin"
os.environ["LD_LIBRARY_PATH"]="/usr/local/GLOBUS-4.0.8/lib:/usr/local/dpm/lib:/usr/local/dpm/lib64:/usr/local/glite/lib"
os.putenv('LD_LIBRARY_PATH',
"/usr/local/GLOBUS-4.0.8/lib:/usr/local/dpm/lib:/usr/local/dpm/lib64:/usr/local/glite/lib")
os.environ["DPM_HOST"]="gsrm"
os.environ["DPNS_HOST"]="gsrm"
proc = subprocess.Popen(['dpns-ls -l /dpm/
ctsf.cdac.org.in/home/OSDD/pubchem',prxy], shell=True,
stdout=subprocess.PIPE,stdin=subprocess.PIPE)
gsrm_output=proc.communicate()[0]
sub_str=gsrm_output.split()
index=8
count=0
str1='<table><tr><td>'+user.email+user.username+"slno"+'</td><td>'+"Gsrm_FileName
"+'</td><td>'+"GSRM_URL"+'</td></tr><tr><td>'
while (index < len(sub_str)):
count=count+1
str1=str1+str(count)+'</td><td>'+sub_str[index]+'</td><td></td><td>'+"/dpm/
ctsf.cdac.org.in/home/OSDD/pubchem/"+sub_str[index]+'</td></tr><tr><td>'
index = index + 9
str1=str1+'</td></tr></table>'
return trans.fill_template( '/sindex.mako',
webapp=webapp,
refresh_frames=refresh_frames,
message=str1,
status='done',
active_view="user" )
@web.expose
created /root/galaxy-dist/templates/sindex.mako
<%!
def inherit(context):
if context.get('webapp'):
webapp = context.get('webapp')
else:
webapp = 'galaxy'
return '/webapps/%s/base_panels.mako' % webapp
%>
<%inherit file="${inherit(context)}"/>
<%namespace file="/messagex.mako" import="render_msg" />
<%def name="init()">
<%
self.has_left_panel=False
self.has_right_panel=False
self.message_box_visible=False
self.active_view="user"
self.overlay_visible=False
%>
</%def>
<%def name="stylesheets()">
${parent.stylesheets()}
<style>
div#center {
padding: 10px;
}
</style>
</%def>
<%def name="title()">Galaxy :: Logout</%def>
<%def name="center_panel()">
${self.body()}
</%def>
<%def name="body()">
%if message:
${render_msg( message, status )}
%endif
</%def>
___________________________________________________________________________________________
Please help!!!!
Regards
Neetu Sharma
10 years, 7 months
