- galaxy-dev - lists.galaxyproject.org

Rendering of multi-selection list
by Michael Römer 25 Feb '14

25 Feb '14

Hi everyone, I'm using the following xml syntax to populate a multi-selection list in our Galaxy Server: <param name="genes" type="select" label="Some list" multiple="true"> <options from_file="some_list.txt"> <column name="value" index="0" /> <column name="name" index="0" /> </options> </param> Depending on the number of entries in the file some_list.txt the list is rendered differently: * with less than 20 entries I get a list displaying all items * with more than 20 entries the list is rendered as a drop-down list * with a lot more (I don't know the exact cutoff, but like 1000+) I get the same rendering as with less than 20 entries I would like galaxy to render the list as a drop-down list independent of the number of entries. Is there a way to do this? Regards, Michael -- Michael Römer, MSc. Bioinf. Abteilung Kognitive Systeme Fachbereich Informatik Wilhelm-Schickard-Institut Sand 1, Raum A312 72076 Tübingen Tel.: +497071/2978970 E-Mail: michael.roemer(a)uni-tuebingen.de

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Test Tool Shed, nightly tests: Error 'unicode' object has no attribute 'get'
by Peter Cock 24 Feb '14

24 Feb '14

Hi guys, Yesterday I made a small tweak to the BLAST+ packages to fix a bash syntax error in the fall back action: https://github.com/peterjc/galaxy_blast/commit/4b2fa1fbf485c4630cb6dc0beaf7… I uploaded this update to the Test Tool Shed packages (all four, BLAST+ 2.2.26, 2.2.27, 2.2.28 and 2.2.29), most of which now unfortunately all show up under "Latest revision: installation errors" (along with the BLAST+ wrappers): Name↓Latest Installable RevisionOwnerncbi_blast_plus<http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositorie…> 39:22b7cdcf4960 (2014-02-20) peterjcpackage_blast_plus_2_2_26<http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositorie…> 5:ebde5fa60194 (2014-02-20) iucpackage_blast_plus_2_2_28<http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositorie…> 2:6f6a8be93479 (2014-02-20) iucpackage_blast_plus_2_2_29<http://testtoolshed.g2.bx.psu.edu/repository/browse_my_writable_repositorie…> 1:c021862e9ea8 (2014-02-20) iuc The BLAST+ 2.2.26 package doesn't seem to show an error: Automated tool test results Test runs 2014-02-20 07:58:47 Tool dependencies TypeNameVersion blast+ package 2.2.26+ Error None The BLAST+ 2.2.27 package seems to have no test results at all. However, the BLAST+ 2.2.28 package has this strange unicode error: Automated tool test results Test runs 2014-02-20 12:48:52 This repository Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' And similarly for BLAST+ 2.2.29, Automated tool test results Test runs 2014-02-20 14:37:58 This repository Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' Error 'unicode' object has no attribute 'get' This is puzzling, since the changes I made to the packages seemed innocuous - making me wonder if something changed in the Test Tool Shed itself? Regards, Peter

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Unicode error manipulation of fastq
by Cantarel, Brandi L. 24 Feb '14

24 Feb '14

Hi, I am testing my newly installed galaxy instance. When I try to use a simple tool like fastq_to_fasta, I get the following error: UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufffd' in position 693: ordinal not in range(256) Anyone know how I can fix this? Thanks! Brandi ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-820-9064 (office) ********************************************************************** This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information.

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Unexpected behaviour when downloading HTML files
by Shian Su 24 Feb '14

24 Feb '14

Hello, After updating my local Galaxy instance to the latest stable release, I've noticed that clicking the floppy-disk download icon on a history item of html type no longer downloads all the files in the relevant directory. Instead it opens up the html page with broken links. However upon going back into the Galaxy page and clicking download for the second time it reverts back to the old behaviour of downloading the html directory in a zip file, from the second time onwards it maintains this behaviour. Is this how it's intended to work? If so then is there intention to remove the ability to download the html directory? Regards, Shian Su

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Re: [galaxy-dev] Reference Genome in snpEff Tool
by Jennifer Jackson 24 Feb '14

24 Feb '14

Hi Xiaofei, It is best to keep replied on the mailing list. First, confirm that you are running the most current version of the Galaxy distribution. This should be true by default if the installation was just performed. https://wiki.galaxyproject.org/DevNewsBriefs https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10 Since you ran into this issue the first time the server was brought up (or this appears to be the case), you may have run into a characterized issue. On the http://getgalaxy.org page, are two work-arounds for installing eggs in under specific usage circumstances. One is for when running without internet access (probably not the issue). The other is for when using Python 2.7 (my best guess as the problem). Both are included about half-way down the wiki page, toward the end of the 'Start it up' section: https://wiki.galaxyproject.org/Admin/GetGalaxy Please review and see if either if these apply, in particular if the second command ("sh run.sh --reload") solves the issue. Again, please keep feedback on the list, so that the developers can assist us going forward as needed, Jen Galaxy team On 2/24/14 9:51 AM, Wang, Xiaofei wrote: > Dear Jen, > > I really appreciate for your reply! > > We decided to install the local Galaxy for this project. But, when I installed it (I followed the instruction on these 2 links, http://gmod.org/wiki/Galaxy_Tutorial_2013 and https://wiki.galaxyproject.org/Admin/GetGalaxy) I got a problem like this: > > $ sh run.sh > Some eggs are out of date, attempting to fetch... > Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched > Traceback (most recent call last): > File "./scripts/fetch_eggs.py", line 37, in <module> > c.resolve() # Only fetch eggs required by the config > File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve > egg.resolve() > File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve > return self.version_conflict( e.args[0], e.args[1] ) > File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) > File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pkg_resources.py", line 576, in resolve > raise DistributionNotFound(req) > pkg_resources.DistributionNotFound: pysam==0.4.2-kanwei-b10f6e722e9a > Fetch failed. > > It seems a problem with the Python '"eggs". But, when I checked the version of Python, it is: > $ python --version > Python 2.7.6 > > Could you help me about what is the problem with the installation? > > Thank you so much! > > Best, > > Xiaofei

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Where to add Account activation
by Danielle Furtado 21 Feb '14

21 Feb '14

I was reading the link: https://wiki.galaxyproject.org/Admin/UserAccounts I wonder where should I add the following line of code in the file universe_wsgi.ini user_activation_on = True I tried adding at the end of the code. I also tried to add in the [app: main] However, it is not functioning. Best Regards, Danielle Furtado.

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With regard to Galaxy tools, a repository should only contain one
by Peter Cock 21 Feb '14

21 Feb '14

Hi all, I've just seen Greg's blog post, "The Galaxy Tool Shed: Best Practices for Populating a Repository" http://gregvonkuster.org/galaxy-tool-shed-best-practices-populating-reposit… One particular point that caught my attention (which I've used as the email title), which seems to signal a move away from "Tool Suites" as a single repository (although they can presumably be emulated by a dummy package defining dependencies on the child tools?). "With regard to Galaxy tools, a repository should only contain one." I look forward to future posts (or emails?) clarifying this... Regards, Peter

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ImportError: No module named json
by Fenglou Mao 20 Feb '14

20 Feb '14

I just upgraded our galaxy server to the latest version, and I got this error in many of the tools: Traceback (most recent call last): File "./scripts/set_metadata.py", line 14, in ? import json ImportError: No module named json And a "find" command below give many a few json eggs, please help. Why Galaxy is not pickung up this json module? (galaxy-env)[galaxy@galaxy galaxy-dist]$ find eggs -name "*json*" eggs/psycopg2-2.5.1_9.2.4_static-py2.6-linux-x86_64-ucs4.egg/psycopg2/_json.py eggs/psycopg2-2.5.1_9.2.4_static-py2.6-linux-x86_64-ucs4.egg/psycopg2/_json.pyc eggs/simplejson-2.1.1-py2.4-linux-x86_64-ucs4.egg eggs/raven-3.1.8-py2.6.egg/raven/utils/json.py eggs/raven-3.1.8-py2.6.egg/raven/utils/json.pyc eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg eggs/boto-2.5.2-py2.6.egg/boto/jsonresponse.py eggs/boto-2.5.2-py2.6.egg/boto/jsonresponse.pyc eggs/boto-2.5.2-py2.6.egg/boto/sqs/jsonmessage.pyc eggs/boto-2.5.2-py2.6.egg/boto/sqs/jsonmessage.py

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Re: [galaxy-dev] Database and FTP setup
by Conrad, Turner Allen 20 Feb '14

20 Feb '14

Thanks, Nate! Got it to run after playing with the postgresql url, table was created, and I began populating it with my admin account. I also prepared the database for ftp by creating a user for lookup. As for proftpd, I have it installed, but am not quite sure what do now. How must I edit the postgresql and proftpd configuration files before changing the galaxy ini? ---------------------------------------------------- 1LT Turner A Conrad, USAR IRR Ph.D. Candidate Graduate School of Biomedical Sciences MED 4.017V Dept. of Microbiology and Immunology 7703 Floyd Curl Drive San Antonio, TX 78229 Email: conradt(a)livemail.uthscsa.edu Office: (210) 567-3947 Cell: (210) 954-0893 On Feb 20, 2014 10:23 PM, Nate Coraor <nate(a)bx.psu.edu> wrote: > > Hi Turner, > > You should be connecting to the database that Galaxy is using, specified in the database_connection option in universe_wsgi.ini. If you have not yet started Galaxy at least once, then the tables will not have been created yet. Once you run Galaxy and the tables have been created, you should be able to connect to that database (galaxydb, or whatever you have set in database_connection) with psql and the GRANT should succeed. > > --nate > > > On Thu, Feb 20, 2014 at 9:49 AM, Conrad, Turner Allen <ConradT(a)livemail.uthscsa.edu> wrote: >> >> Hi, >> >> >> I'm not experienced with postgres and ftp and am thus having difficulties setting up an ftp server on my local Galaxy instance, but it is essential as our files are all over 2GB. The admin support page (https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP) is a little fuzzy on the details. I'm currently running the server out of Ubuntu 13.10 desktop both physically and via SSH. So far, I've created a local account postgres with a psql database galaxydb and user galaxyftp, but I can't figure out whether the galaxy_user table is supposed to exist, needs to be created, nor how to add this information to the database_connection option in universe_wsgi.ini. ALTER ROLE has been completed successfully, but I get the error ERROR: relation "galaxy_user" does not exist upon attempting GRANT SELECT ON. Is there a simple explanation of how to complete this task and get the proftpd server up and running for Ubuntu? Please assume proftpd is installed, but not configured, the database is in the state described above, and I am starting with sudo su - postgres followed by psql galaxydb . >> >> >> >> Turner Conrad >> UTHSCSA >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >

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Database and FTP setup
by Conrad, Turner Allen 20 Feb '14

20 Feb '14

Hi, I'm not experienced with postgres and ftp and am thus having difficulties setting up an ftp server on my local Galaxy instance, but it is essential as our files are all over 2GB. The admin support page (https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP) is a little fuzzy on the details. I'm currently running the server out of Ubuntu 13.10 desktop both physically and via SSH. So far, I've created a local account postgres with a psql database galaxydb and user galaxyftp, but I can't figure out whether the galaxy_user table is supposed to exist, needs to be created, nor how to add this information to the database_connection option in universe_wsgi.ini. ALTER ROLE has been completed successfully, but I get the error ERROR: relation "galaxy_user" does not exist upon attempting GRANT SELECT ON. Is there a simple explanation of how to complete this task and get the proftpd server up and running for Ubuntu? Please assume proftpd is installed, but not configured, the database is in the state described above, and I am starting with sudo su - postgres followed by psql galaxydb . Turner Conrad UTHSCSA

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