February 2013 - galaxy-dev - lists.galaxyproject.org

Error with local toolshed and remote user authentication: "HTTPError: HTTP Error 401: Authorization Required"
by Carlos Borroto 14 Feb '13

14 Feb '13

Hi, I would like to use Apache LDAP to authenticate a local toolshed. Configuring community_wsgi.ini wasn't a problem and I can now login into the local toolshed with my institution active directory credentials. The same way I do for the local Galaxy. I did have to add remote_user_maildomain as it wasn't there and I needed it. Maybe this is something that could be added in the next release. The problem is when I try to install a tool from this toolshed I get: URL: http://galaxy-bfx.brel.local/admin_toolshed/prepare_for_install?tool_shed_u… File '/local/opt/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/local/opt/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/local/opt/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/local/opt/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/local/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/local/opt/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/local/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/local/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 208 in decorator return func( self, trans, *args, **kwargs ) File '/local/opt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1177 in prepare_for_install response = urllib2.urlopen( url ) File '/usr/lib64/python2.6/urllib2.py', line 126 in urlopen return _opener.open(url, data, timeout) File '/usr/lib64/python2.6/urllib2.py', line 397 in open response = meth(req, response) File '/usr/lib64/python2.6/urllib2.py', line 510 in http_response 'http', request, response, code, msg, hdrs) File '/usr/lib64/python2.6/urllib2.py', line 435 in error return self._call_chain(*args) File '/usr/lib64/python2.6/urllib2.py', line 369 in _call_chain result = func(*args) File '/usr/lib64/python2.6/urllib2.py', line 518 in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 401: Authorization Required Is there any trick I could do with Apache to let this go through? This is my current Apache configuration: <VirtualHost *:80> ServerAdmin carlos.borroto(a)gmail.com ServerName toolshed-bfx.brel.local:80 <Proxy http://localhost:9009> Order deny,allow Allow from all </Proxy> RewriteEngine on <Location "/"> AuthName "Galaxy Toolshed BFX" AuthType Basic AuthBasicAuthoritative off AuthBasicProvider ldap AuthzLDAPAuthoritative off AuthLDAPURL "ldap://ad.brel.local/OU=BREL,DC=brel,DC=local?sAMAccountName?sub" AuthLDAPBindDN "MASKED" AuthLDAPBindPassword "MASKED" Require valid-user # Set the REMOTE_USER header to the contents of the LDAP query response's "uid" attribute RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e XSendFile on XSendFilePath / </Location> RewriteRule ^/static/style/(.*) /local/opt/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /local/opt/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /local/opt/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /local/opt/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /local/opt/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:9009$1 [P] ErrorLog logs/toolshed-bfx.brel.local-error_log CustomLog logs/toolshed-bfx.brel.local-access_log common </VirtualHost> As always any help will be highly appreciated, Thanks, Carlos

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jobs don't get killed when histories deleted?
by Anthonius deBoer 14 Feb '13

14 Feb '13

Hi, I am continue to struggle with the proccess of killing jobs that run on the SGE cluster when deleting histories. I would assume that jobs get removed from the queue when a history they are part of is deleted but in most cases, the jobs stay on the cluster and are not killed.... I also never have been able to get the kill jobs in the admin section to work (using the 8-Feb version)...It just sites there, returns and the jobs are still there on the cluster and still there in the database.... Is there anything in the database I can do to really kick out those jobs? Thanks Thon

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Environment variables reset after manually restarting Galaxy
by Joachim Jacob |VIB| 14 Feb '13

14 Feb '13

Hello all, After a *reboot* of our Galaxy server, the environment variables are set correctly. However, after *restarting* the Galaxy process on a running server, by logging in as Galaxy and running the init script on CentOS as "service galaxyd restart", the environment variables seems to be messed up After this manual Galaxy restart, some tools are not found, apparently caused by a modification of the environment variable PATH. Can somebody provide me perhaps with insight on what is causing this, and how to avoid this? My environment variables are set in /etc/profile.d/galaxy_environment_setup (which is a symbolic link to -> /home/galaxy/environment_setup ) Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Reloading a tools configuration does not seem to actually work
by Anthonius deBoer 14 Feb '13

14 Feb '13

Hi, I find that reloading a tool's configuration file does not really work. First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)... But when I try to run my tool, the old bug is still there... I am using proxy server so something may still be cached, but I have to restart my server for it actually to pick up the changes... Any ideas? Thon

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Re: [galaxy-dev] Problems linking Data inside Galaxy
by Nate Coraor 14 Feb '13

14 Feb '13

On Feb 13, 2013, at 6:42 PM, Gaueko Erge wrote: > Hi Nate, > > Thank you for your reply. After a lot of trying I was able to figure this out > > Entries in my alignsec.loc file were pointing to: > > seq AaegL1 /db/galaxydb/AaegL1/seq/ > seq AgamP3 /db/galaxydb/AgamP3/seq/ > > and not to: > > seq AaegL1 /db/galaxydb/AaegL1/seq/AaegL1.2bit > seq AgamP3 /db/galaxydb/AgamP3/seq/AgamP3.2bit > > As required for this this work > > I guess, I was confused and/or did not understand the instructions well. Also, I was confused because I thought that the '2bit' files had to be present in the 'twobit.loc' file and not in alignsec.loc > > Honestly, I am still trying to mentally sort out what datasets are used by ucsc browser (local installation) and what datasets are used only by galaxy. AND how to proceed to upload my own genomes to both galaxy and to my local deployment of ucsc browser Hi Gaueko, I'm glad to hear it's working. If you have any suggestions on how to improve our documentation for this, please let us know. --nate > > Thanks > > --G > > > On Wed, Feb 13, 2013 at 1:27 PM, Nate Coraor <nate(a)bx.psu.edu> wrote: > On Feb 12, 2013, at 10:49 AM, Gaueko Erge wrote: > > > Hi, > > > > I have followed, carefully, the instructions posted in:http://wiki.galaxyproject.org/Admin/Data%20Integration > > > > Yet, despite my best efforts when I get, say all exons from hg19 build and try to their fetch sequences, galaxy tells me that the sequences for hg19 are not there > > > > I find this surprising because I have downloaded: > > > > rsync://datacache.g2.bx.psu.edu/indexes/ > > rsync://hgdownload.cse.ucsc.edu/gbdb/ > > rsync://hgdownload.cse.ucsc.edu/goldenPath/vicPac1/bigZips > > > > databases and added the correct paths to the 'alignseq.loc' file > > Hi Gaueko, > > It'd be helpful if you could provide us with the entry from your alignseq.loc file. Also, you may want to verify that your alignseq.loc contains only tabs between the fields, not spaces. > > --nate > > > > > Any ideas will be appreciated > > > > Thanks > > > > --G > > ___________________________________________________________ > > 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/ > >

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hg19 reference gnome for Tophat2
by Sachit Adhikari 14 Feb '13

14 Feb '13

I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index with the files: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.rev.1.bt2 genome.rev.2.bt2 While adding the reference gnome, I need to edit bowtie2_indices.loc Shall I replace: /orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Thanks, Sachit

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How to redirect output of all the galaxy tools to another directory?
by Sachit Adhikari 14 Feb '13

14 Feb '13

I want to redirect all the output of Galaxy to another directory(actually a external hard drive with full write access). How can I do that? Thanks

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Incomplete tophat2 output
by Sachit Adhikari 14 Feb '13

14 Feb '13

Tophat2 output on accepted hits, deletions and insertions is fine whereas splice junctions output is only: track name=junctions description="TopHat junctions" I am running tophat2 with hg19 reference genome? What might be the problem?

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Overwriting tools directory?
by Amanda Zuzolo 14 Feb '13

14 Feb '13

Since I can't find this on any of the wikis: when updating Galaxy through mercurial, is the tools directory affected? Our instance has backups of the directory, but I want to know whether I will have to take care of them when I pull down the latest release. Thanks in advance. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity

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Exception seen in update_manager.py; global name 'suc' is not defined
by Anthonius deBoer 13 Feb '13

13 Feb '13

Hi, I see this in the log file... this really "suc"ks :) Thon Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib64/python2.6/threading.py", line 532, in __bootstrap_inner self.run() File "/usr/lib64/python2.6/threading.py", line 484, in run self.__target(*self.__args, **self.__kwargs) File "/mnt/ngs/analysis/svcgalaxy/galaxy-dist/lib/galaxy/tool_shed/update_manager.py", line 28, in __restarter if self.check_for_update( repository ): File "/mnt/ngs/analysis/svcgalaxy/galaxy-dist/lib/galaxy/tool_shed/update_manager.py", line 37, in check_for_u pdate tool_shed_url = suc.get_url_from_repository_tool_shed( self.app, repository ) NameError: global name 'suc' is not defined

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