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blastn: Error: NCBI C++ Exception
by Berner, Thomas 13 Jun '13

13 Jun '13

Hi guys, another error appeared after we installed NCBI BLAST + to our local Galaxy instance and wanted to test it. After uploading some testdata to our history we tried to run blastn on it and got the following error: Fatal error: Matched on Error: Error: NCBI C++ Exception: "/opt/galaxy/galaxy-dist/database/tmp/tmphx2DHp/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. With some testing around we figure out the problem: ./blastn -query ~/test.fasta -db nt -task blastn -evalue 0.001 -out ~/out2.txt -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -num_threads 8 Doesn't work until we replaced the "num_threads 8" like it is written in the original "ncbi_blastn_wrapper.xml" with "num_threads 1" Editing the .xml also solved the problem within the galaxy surface. Now my question is, is there any other workaround without editing the" ncbi_blastn_wrapper.xml"? Searching in the documentation and the mailing list, I did not find anything about this. We believe this could be of common interest. It would be great if anybody could comment on this. Thanks a lot, Thomas

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database upgrade crashes after upgrade to the June 3, 2013 Galaxy release
by Christophe Antoniewski 12 Jun '13

12 Jun '13

Hi, Sorry to bother again, but we have now a problem with the last release of galaxy-dist The lack of a python module asked by a python eggs seems to interrupt our postgresql database upgrade from version '114' to '115' sh manage_db.sh upgrade Traceback (most recent call last): File "./scripts/manage_db.py", line 13, in <module> from migrate.versioning.shell import main File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 12, in <module> from migrate.versioning import api File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 33, in <module> from migrate.versioning import (repository, schema, version, File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/repository.py", line 13, in <module> from migrate.versioning import version, pathed, cfgparse File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/version.py", line 10, in <module> from migrate.versioning import pathed, script File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/pathed.py", line 11, in <module> from migrate.versioning.util import KeyedInstance File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 7, in <module> from decorator import decorator ImportError: No module named decorator Any idea ? Thanks Chris -- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org

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Galaxy Security Notification
by Nate Coraor 12 Jun '13

12 Jun '13

A security vulnerability was recently discovered by Björn Grüning with Galaxy's "user impersonation" feature that can expose an administrator's active history to users whom they impersonate. Only Galaxy instances with `allow_user_impersonation = True` set in their configurations are affected, and only if an administrator makes use of the impersonation feature. By default, user impersonation is disabled. A fix (id: 9d42f1e32efb) has been provided in the stable branch of Galaxy. To apply the fix, ensure you are on the stable branch and upgrade to the latest changeset: % hg branch stable % hg pull -u For Galaxy installations on relatively old versions that administrators are not yet ready to upgrade, there are three workarounds. First, the patch can be downloaded and applied manually: % wget -o security.patch https://bitbucket.org/galaxy/galaxy-central/commits/9d42f1e32efb654fda1e011… and then: % hg patch security.patch or: % patch -p1 < security.patch Second, the impersonation feature can be disabled by setting the following option in Galaxy's configuration file: allow_user_impersonation = False In all of the above cases, the Galaxy server process(es) must be restarted for the change to take effect. Third, the feature can be left enabled and unpatched, and the vulnerability can be worked around by educating administrators who use the feature. As long as a new history is created by the administrator prior to switching to the impersonated user, no data will be exposed to the impersonated user. --nate Galaxy Team

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Re: [galaxy-dev] Toolshed bug related to readme files
by Lance Parsons 12 Jun '13

12 Jun '13

I'm running the latest stable. The 500 error seems to be coming from the toolshed. Do you also get a 500 error at the toolshed URL in my previous message? There is nothing other than standard info line from the request in my pasted log. I'm not able to get to the log right now, but I'll send it once I get a chance tomorrow. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University -------- Original message -------- From: Greg Von Kuster <greg(a)bx.psu.edu> Date: 06/11/2013 10:00 PM (GMT-05:00) To: Lance Parsons <lparsons(a)princeton.edu> Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] Toolshed bug related to readme files Hi Lance, What version of Galaxy are you running? Is the 500 error coming from your Galaxy server or the tool shed server? Can you send the relevant information from your Galaxy paster log when attempting to reinstall? Thanks, Greg Von Kuster On Jun 11, 2013, at 3:52 PM, Lance Parsons <lparsons(a)princeton.edu> wrote: > I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard). > > When I attempt to reinstall (after successfully uninstalling) I get a 500 error. After a bit of poking around, it seems that this URL generates the 500 error: > > http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner… > > Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aa… > > > -- > Lance Parsons - Scientific Programmer > 134 Carl C. Icahn Laboratory > Lewis-Sigler Institute for Integrative Genomics > Princeton University > > ___________________________________________________________ > 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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Galaxy on Cluster - how to set -a flag with username
by greg 12 Jun '13

12 Jun '13

In our local galaxy install we want the cluster jobs to be run from the galaxy user but we want to include a -a [account name] to our grid software bills properly. Here's what I currently have in universe.wsgi: default_cluster_job_runner = drmaa://-V -pe batch 8/ What I want is something like this: default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/ Is this possible? Thanks, Greg

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Recently Used Histories
by Jonathan Strickland 12 Jun '13

12 Jun '13

Hello all! I've recently started using Galaxy, and it's a fantastic piece of software. However, I had a question about a possible feature, and any suggestions on how to implement it. My use case involves working with a lot of histories, and I need to jump back and forth between them fairly frequently. However, it's a bit inconvenient to have to click on the "Options" button on the rightmost pane, "Saved Histories" in the drop-down menu, and select my history on the main pane. An easier way to switch between histories that were recently used could definitely benefit me, and perhaps other people too. I propose an easily accessible list with links to the 5 most recently visited histories. I took a look at the source, but as I'm unfamiliar with Django and the Galaxy codebase, I thought it might be best to come here for advice. My initial thought was to show the last 5 most recently updated histories underneath the "History Lists" in the options menu. However, that would probably cause trouble when working when Shared Histories that other people are working on, jumping up to the top of the list whenever anyone edits them. The best solution I could think of was to have some sort of list of the histories visited. When the user selects a history, that history is pushed to the top of the stack, and if there are more than 5 items in the stack, the least recent history is popped off. Ideally, the user wouldn't need to go back to the "Saved Histories" or "Histories Shared With Me" grid when working with a few different histories at once. I'm also not sure where the user's state is stored, so I don't know where I would put this variable. I'm also not sure if there's any hooks or anything when selecting a history that I could take advantage of to push it to the top of the user's stack. An issue with this approach is that an item from a history may be open on the main pane, and the user can select another history without going to either grid of histories. This problem doesn't currently occur, because the only way to select a different history is by opening up the history list on the main screen. The main pane needs to be changed to something else upon changing histories, but I don't have any ideas as to what would be best. Perhaps the default "Analyze Data" screen? Sorry for so many questions! Any answers or suggestions would be much appreciated :) I'm also curious if anyone would benefit from this feature besides myself!

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Toolshed bug related to readme files
by Lance Parsons 12 Jun '13

12 Jun '13

I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard). When I attempt to reinstall (after successfully uninstalling) I get a 500 error. After a bit of poking around, it seems that this URL generates the 500 error: http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner… Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aa… -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Trackster error: not able to find the chrom len file
by Joachim Jacob | VIB | 11 Jun '13

11 Jun '13

Dear all, I updated to the latest Galaxy stable code, and updated the datatypes_conf.xml. Trackster displays an error after opening a saved view: *********************** Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be opened. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , No such file or directory *********************** In my universe_wsgi.ini I point to the correct directory where I keep my chrom len files. # Directory where chrom len files are kept, currently mainly used by trackster len_file_path = /mnt/referencedata/trackster Thanks for any advice, Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Pasted text in upload.py
by Daniel Gorelik 11 Jun '13

11 Jun '13

Hello, I am trying to understand how the upload.py file works. I have already spent a long time trying to figure this out, but I just cannot at all understand where, for example, a pasted text input is saved. Let's say, for example, I wanted to make any pasted text input all caps. Where would I put .upper? Thank you, Daniel Gorelik

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Trackster set display mode - Output looks all the same
by Linda Cham 11 Jun '13

11 Jun '13

Hi. Running Galaxy stable_2013.06.03 version on RH6.2 with postgresl db. Generated bam and vcf file to view under Trackster. Set up trackster by following http://wiki.galaxyproject.org/Learn/Visualization directions. No matter what I choose for "Set display mode", all I see is blocks of color for the vcf (is that the INTENSITY mode?) and a line for the BAM file which doesn't seem to be what the directions above for the Histogram, Line, Filled, and Intensity are supposed to look like. Not sure what the output supposed to look like so can't tell if it is correct or not. 1- Should the "Set display mode" give out different output? 2- What might be the issue if all I see are the same output or maybe the output displayed is totally incorrect? Might there be some trackster setup that I might be missing for it to draw incorrectly? What is shown: Not sure if the 2 images that I had inserted above will be viewable after I send out the request. Thanks in advance. Linda

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