[galaxy-dev] Change Manage data Libraries
Hello everyone, I'm trying to change some options in the Manage data Libraries.Especially in the Server Directory, by clicking the Upload directory of file in Upload option. So I've changed universe_wsgi.ini file and add for library_import_dir my directory. The problem is that I can see only one directory link in Galaxy. I've tried to write two times library_import_dir but it's not working, only the last directory is taken into account : library_import_dir = /sequences/fasta/maize/ library_import_dir = /home/***/blastdb_loc/ Also tried to insert a comma but it appears in Galaxy : library_import_dir = /sequences/fasta/maize/, /home/***/blastdb_loc/ Someone has an idea ?Advance thanks, Siva ___ 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] problem after last upgrade
Dear galaxy,
I have upgraded my galaxy-dist with last official version ( upgrade: %
hg pull -u -r 40f1816d6857 ). I also upgraded database (sh manage_db.sh
upgrade).
now I have problem with running galaxy instance and this is what I get:
/home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
from csamtools import *
python path is:
/home/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg,
/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/home/galaxy/galaxy-dist/lib, /usr/lib/python2.6,
/usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk,
/usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload,
/usr/local/lib/python2.6/dist-packages,
/usr/lib/python2.6/dist-packages/PIL,
/usr/lib/pymodules/python2.6/gtk-2.0,
/usr/lib/python2.6/dist-packages/gst-0.10,
/usr/lib/python2.6/dist-packages/gtk-2.0,
/usr/lib/pymodules/python2.6/ubuntuone-storage-protocol,
/usr/lib/pymodules/python2.6/ubuntuone-client,
/usr/lib/python2.6/dist-packages, /usr/lib/pymodules/python2.6
galaxy.model.migrate.check DEBUG 2012-03-14 16:29:23,928 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-03-14 16:29:24,000 At database
version 93
galaxy.tool_shed.migrate.check DEBUG 2012-03-14 16:29:24,007 psycopg2
egg successfully loaded for postgres dialect
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 82,
in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /home/galaxy/galaxy-dist/lib/galaxy/app.py, line 37, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File
/home/galaxy/galaxy-dist/lib/galaxy/tool_shed/migrate/check.py, line
42, in verify_tools
db_schema = schema.ControlledSchema( engine, migrate_repository )
File
/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 24, in __init__
self._load()
File
/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 42, in _load
data = list(result)[0]
IndexError: list index out of range
best,
michal
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[galaxy-dev] Exporting worflow to local instal
Hi, I would like to download/export my workflows from the Galaxy main to a local install at my institution. When I use the URL method, I get the following error message: Data at 'http://main.g2.bx.psu.edu/u/muehlsch12/w/imported-tophat---cuffdiff-paired-end-fastq ' does not appear to be a Galaxy workflow Message: No JSON object could be decoded: line 1 column 0 (char 0) When I want to download a workflow to my local machine, I get a server error (Duplicate headers received from server). The local install does not recognize publicly published workflows, so that step won't work either. Thanks for your help, Danny The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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] Error starting Galaxy after update of March 2012
Nate Coraor wrote: On Mar 13, 2012, at 11:08 AM, Alban Lermine wrote: Hi Alban, Is your Galaxy server behind a firewall or without network access such that it cannot access http://eggs.g2.bx.psu.edu/ ? What happens if you run `python scripts/fetch_eggs.py` by hand? Is there a way to downgrade Galaxy? Yes, in most cases you can downgrade with `hg update -r old changeset id`. --nate Thanks by advance for your answer.. Alban -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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, Thanks for your fast answer.. I run fetch_eggs.py by hand, here is the return: Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.6.egg Removed conflicting egg: galaxy_dir/galaxy-dist/eggs/boto-1.8d-py2.6.egg I tried then to start Galaxy, and I also have a new error message: Traceback (most recent call last): File /bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/web/buildapp.py, line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/app.py, line 24, in __init__ self.config.check() File /bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/config.py, line 254, in check raise ConfigurationError( Unable to create missing directory: %s\n%s % ( path, e ) ) ConfigurationError: Unable to create missing directory: ./../shed_tools [Errno 13] Permission denied: './../shed_tools' It seems it's now only a permission problem.. (I only have rights on galaxy-dist directory), I will ask our system engineer to rerun update.. Hi Alban, You can fix this one by changing the path to the shed_tools directory in shed_tool_conf.xml. It can be any directory you can write to, but should not be underneath the galaxy-dist directory. --nate Alban -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 It's working again, great thanks, Alban -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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] Authentic problem about uploading files to GenomeSpace
Hi Hanfei, I would strongly suggest against having an input field for a password in a Tool, it is not secure at all. Also, as an FYI, we're working locally on GenomeSpace interoperability functionality and it should be released relatively soon, so you may want to hold off on your efforts for now (but you don't have too). Thanks for using Galaxy, Dan On Mar 14, 2012, at 1:24 AM, Hanfei Sun wrote: Hi, I'm trying to write a tool that can send data(upload) from Galaxy to GenomeSpace. I've developed a prototype that can be accessed by the following link: http://cistrome.org/ap/tool_runner?tool_id=send_genomespace (It locates at Galaxy Toolbox- Get Data - Send data to Genome Space) But the current problem is, the Galaxy server doesn't has the authentic information (user-name, password or token) of Genome Space. So the user need to submit the GenomeSpace account and password to the Galaxy server. What's more, for every time he wants to do the uploading, he need to submit the GenomeSpace password again to Galaxy because Galaxy can not hold on this information. It's quite inconvenient and unsafe to input the password again and again. (If Galaxy can bind a user's Galaxy account to his Genome Space account, this problem may be solved. But as far as I know, this is not available currently.) Does anyone know how to deal with this problem? Thanks! -- Best wishes, Hanfei Sun ___ 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] Change Manage data Libraries
On Wed, Mar 14, 2012 at 6:07 AM, Sivasangari NANDY nsi...@hotmail.com wrote: I've tried to write two times library_import_dir but it's not working, only the last directory is taken into account : library_import_dir = /sequences/fasta/maize/ library_import_dir = /home/***/blastdb_loc/ Hi Siva, You could have only one import directory in universe_wsgi.ini and place links to other directories in the configured directory. Galaxy will let you select from which directory(or link to directory) you want to import files when importing. Hope it helps, Carlos ___ 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] [galaxy-user] How to Pass Parameter
On Tue, Mar 13, 2012 at 2:15 PM, La Chi the_man.in...@yahoo.com wrote: hi galaxy developers , i have developed this parameter in xml file and i am passing tl value to a function which is present in my python file , but when i select its type=text , it shows a text field with tl , all i want to know how can i pass kb value without showing text field on galaxy. thanks param name=site type=text label=site for value=tl help=Enter tl / Hi, I'm not quite sure I understood your question, but I wonder if type=hidden is what your looking for: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_tag_set Hope it helps, Carlos ___ 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] Galaxy: enable uploading via FTP
On Mar 12, 2012, at 5:15 PM, jiechenable1...@gmail.com wrote: Dear Nate, Sorry to trouble you. I know that you are busy, but this problem has annoyed me for couple days. Please help. I want to enable uploading via ftp for my local Galaxy instance. I followed the instructions under the wiki page strictly. However it doesn't work. What i did: 1) set the directive ftp_upload_dir = /home/jjc25/central/galaxy-central/database/ftp/ in the universe_wsgi.ini 2)set the directive ftp_upload_site = 127.0.0.1 3)created the database user galaxyftp and granted select access to it 4)copied and pasted the proftpd configuration file on the page (http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) and only modified the directive SQLConnectInfo galax...@dbserver.example.org dbuser dbpassword to my own settings, which is SQLConnectInfo galaxydb@localhost galaxyftp mypassword 6)restart proftpd by sudo service proftpd restart - here comes the error: Fatal: unknown configuration directive 'SQLPasswordEngine' on line 43 of '/etc/proftpd/proftpd.conf' I can't restart the ftp server because some unknown reasons. Can you help me out please. A lot of thanks. By the way, i am using the copy of Galaxy with id : changeset: 6818:48b64ce958b4 Look forward to your reply. Thanks, JIE CHEN Hi Jie, It looks like your ProFTPd server does not include the mod_sql_passwd module. We compile ours by hand, so I can't tell you whether or not any of the prepackaged versions for Linux have a way to install a precompiled version of that module. I do see that there is not a separate package for proftpd-mod-sqlpasswd (or similar) in Debian, but that you might be able to build it if you install proftpd-dev. I've updated the wiki page to include information about how we compile ProFTPd. Please send questions to the mailing list rather than directly to individual people on the team. There are others who may be able to answer your question in a timelier manner (and the community as a whole can benefit from the public response). --nate ___ 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] Galaxy server configuration question
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote: Dear Nate, I have a follow up question for you. If I move galaxy out of my DocumentRoot /var/www/html to /home/galaxy/galaxy-dist , how to set up my Apache server, that is, httpd.conf file so I can access the website http://server/galaxy? I have a website http://server for something else. I've tried different ways but no luck. Hi Huayan, The configuration for this is shown under the heading: Serving Galaxy at a sub directory (such as /galaxy) On the Apache Proxy wiki page: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy --nate Best, Huayan On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote: On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote: Hi Nate. I am ok now. The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved. Hi Huayan, I've updated the wiki to refer to galaxy-dist rather than galaxy_dist. Sorry for the confusion. I would suggest moving galaxy out of /var/www/html. From the documentation: Please note that Galaxy should never be located on disk inside Apache's DocumentRoot. By default, this would expose all of Galaxy (including datasets) to anyone on the web. Galaxy is a proxied application and as such, only the static content like javascript and images are served directly by Apache (and this is set up with the RewriteRules), everything else is passed through to the Galaxy application via a proxied http connection. Right now I could presumably use the URL http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a dataset directly. --nate Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: Hi Nate, I removed the proxy section in httpd file and got the following screenshot. It seems working but not in the way we expected. I will keep looking for the solution but do you know how to fix it? It seems to say, the file .../static/welcome.html is missing or something like that. Thanks, Huayan Screen Shot 2012-02-13 at 11.37.57 AM.png On 10 Feb, 2012, at 10:28 AM, Huayan Gao wrote: Hi Nate, Yes, I did follow the instructions. But I came to the question in httpd.conf file. I put galaxy-dist under my document root which is /var/www/html/. When my server is up, I can access my UCSC genome browser mirror site through my ip address, for example, http://61.244. xxx.xxx. Then how should I set up in httpd.conf file so I can access galaxy using my ip address, for example, http://61.244. xxx.xxx/galaxy? Thanks, Best, Huayan On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote: On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote: Dear Sir or Madam, I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site. The mirror site works well. I installed the galaxy in the same server. Now my question is: how to set up httpd.conf file so I can access both websites(UCSC Genome Browser, and Galaxy) remotely? Hi Huayan, Have you consulted the production server documentation? http://usegalaxy.org/production --nate Best, Huayan ___ 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] Error while uploading
On Mar 12, 2012, at 2:23 PM, Fields, Christopher J wrote: You can change the default location of tmp files by modifying the environment; we ran into this with samtools directly dumping temp sort files to a local node, causing the job to shut down. Setting TMPDIR worked for me. Hi Chris, Thanks for pointing this out, I've added it to the cluster wiki page: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Galaxy_Configuration --nate chris On Mar 11, 2012, at 5:10 PM, Dorset, Daniel C wrote: Hi Luciano, I had a similar problem with our local instance of Galaxy. In our case, the /tmp directory was filling up, causing the job to abort. We had Galaxy running on a partition with tons of disk space, but the partition on which /tmp was located had substantially less free disk space. Try running the df command from the Linux command line. If you don't know how to interpret its output, let me know. Certain tasks that run on behalf of Galaxy, like gzip for decompressing large datasets, will store intermediate temporary data in /tmp instead of a subdirectory within your Galaxy installation. Let me know if that solves your issue, Dan Message: 1 Date: Sat, 10 Mar 2012 17:25:38 -0600 From: Luciano Cosme cosme.sim...@gmail.com To: Galaxy-dev galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Error while uploading Message-ID: camasfsjdm0udcivqk7p-mpijr8ualxe0zx7szug4upsqj_n...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I uploaded 11 files today (1 to 2Gb compressed files) to my local instance without a problem (as admin). Then I got this error message below and it get stuck at This dataset is uploading and I could not upload the last files. Is there anything I can do to solve it? What I notice is that I can still upload small files, before I concatenate them. I have 15 time points and some of them have up to 20 files, so it is easier to concatenate them and them upload. Thank you. Luciano ___ 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/ ___ 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/
