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

WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
by Luobin Yang 24 Jan '13

24 Jan '13

Hi, I ran into this error and I found the following thread discussing the problem, interestingly, for my system, the computer node runs the same Python version as the head node, but with a newer OS version, but it also generates this error. Does this mean the Galaxy system requires the computer nodes in a cluster to have the same version of OS and the same version of Python? http://comments.gmane.org/gmane.science.biology.galaxy.devel/3188 Luobin

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Re: [galaxy-dev] filtering a <param> of type 'data' so only one type is available
by Dan Tenenbaum 24 Jan '13

24 Jan '13

On Wed, Jan 23, 2013 at 4:03 PM, Ross <ross.lazarus(a)gmail.com> wrote: > Hi, Dan > Glad it worked and thanks for pointing out a more general mimetype - does > any one else (other than me) want to vote to add > <datatype extension="rda" type="galaxy.datatypes.binary:Binary > mimetype="application/x-gzip" subclass="True" /> > to datatypes_conf.xml.sample permanently ? > I do. This would be great as I am automating the creation of galaxy tools and I'd like to be able to enable this feature without requiring (either manual or programmatic) editing of datatypes_conf.xml. Note that serialized R objects also sometimes have the .RData extension -- both are valid -- so it would be good to support that as well. But now that I think about it, serialized objects are not always gzip files--depending on the value of the 'compression' flag used with the save() function, it may be gzip, bzip, xz, or even ascii! So maybe the mime type should be changed back to something different, like application/x-rlang-transport as you suggested. I tried this and it seemed to work; It did the filtering I wanted and I was still able to download a history item with this type. Dan Thanks, Dan > > On Thu, Jan 24, 2013 at 10:58 AM, Dan Tenenbaum <dtenenba(a)fhcrc.org> wrote: >> >> On Wed, Jan 23, 2013 at 3:51 PM, Ross <ross.lazarus(a)gmail.com> wrote: >> > Hi, Dan. >> > Using format="rda" will restrict the list to history items of the 'rda' >> > datatype - but ONLY if the rda datatype has been defined! >> > The easiest way to do that is to define a new datatype in >> > datatypes_conf.xml >> > and since rData is binary, you should subclass binary. >> > Something like (untested - especially the mimetype !) >> > <datatype extension="rda" type="galaxy.datatypes.binary:Binary" >> > mimetype="application/x-rlang-transport" subclass="True" /> >> > might work. A server restart is always required to load any new >> > datatypes. >> > Good luck! >> > >> >> It works! I changed the mime type to application/x-gzip, since >> serialized R objects are gzipped. >> >> Thanks, >> Dan >> >> >> > >> > >> > On Thu, Jan 24, 2013 at 10:41 AM, Dan Tenenbaum <dtenenba(a)fhcrc.org> >> > wrote: >> >> >> >> Hi, >> >> >> >> I have a tool wrapper with a <param> of type="data". >> >> >> >> Currently, this renders as a text box with a drop down list that has >> >> 52 items in it (the number of things I have in my history, I guess). >> >> >> >> I'd like to filter this list so that only some items in the history >> >> (in my case any item whose name ends with '.rda') are shown in this >> >> dropdown. >> >> >> >> It seems like maybe the 'format' parameter to the 'param' tag is what >> >> I want, but: >> >> 1) I tried format="rda" and that didn't seem to change anything. >> >> 2) "rda" is not in the datatypes.conf file which the documentation >> >> suggests is required? >> >> >> >> (.rda is an extension used for serialized R objects.) >> >> >> >> The tool I'm working on only accepts rda files as input and the reason >> >> I'm asking for this is that it is all too easy to accidentally feed it >> >> a file of some other type. If the dropdown could be filtered so that >> >> only items which will work with the tool are shown, that would be >> >> great. >> >> >> >> Is there a way to do that? >> >> Thanks, >> >> Dan >> >> ___________________________________________________________ >> >> 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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minimum AWS resources for TopHat?
by Andrew Norman 23 Jan '13

23 Jan '13

Hi all I'd like to use AWS EC2 cluster to run Galaxy TopHat to analyze the RNA seq data for my project. I'm trying to price out the resources that I'll need to do this, but I don't have any experience setting up clusters, virtual or real, so I'd like to get the insight of someone who has done this. I have studied the wiki page dedicated to this topic ( http://wiki.galaxyproject.org/CloudMan/AWS/CapacityPlanning) but I don't know how many worker nodes I'll need, and I will just be doing my personal analysis with this cluster (only one TopHat analysis at a time). Can anyone help me out with this? Thanks! Andy

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Job Update Time rollover at 24 hours
by Eric Enns 23 Jan '13

23 Jan '13

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different path for galaxy in cluster
by Hagai Cohen 23 Jan '13

23 Jan '13

Hi, I have a problem with my galaxy local installation working with a cluster. On the server my galaxy dir path is X, but on the cluster it is Y (same directory but different soft links). Is it possible to config the path of the galaxy installation (GALAXY_DIR) which will be send to the nodes? Thanks, Hagai

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Associate a user with a Galaxy user via e-mail like OpenID does
by Zinonas Antoniou 23 Jan '13

23 Jan '13

Hello, I have the connection using OAuth and I get the email of a user from other platform. Next, I want to associate this user with a user of Galaxy, like the OpenID does. Can anyone describe me explicitly the procedure should I do? What files should I change? Thank you in advance, Zinon

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Enhancing tool id="subtract_query1"
by Joachim Jacob 23 Jan '13

23 Jan '13

Hi all, One of our users had a problem, that the subtract datasets tool did not behave. She had just uploaded two datasets, one column each (actually in txt format), one with ~300000 lines, another with 106, and used the subtract tool. It did not work because of trailing white spaces (spaces, tabs and EOL) in the second file. Looking at the code, I had made a small adjustment then: adding a line: line = line.rstrip() (Line 32 in ~/galaxy-dist/tools/new_operations/subtract_query.py). Anyway, how to proceed that this fix is included in Galaxy main? I understand that these tools eventually will be migrated to the toolshed? Is it useful to do a pull request for this small enhancement? Or can somebody of the devteam add this patch? 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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Upgrade Python to a newer version.
by Luobin Yang 23 Jan '13

23 Jan '13

Hi, Galaxy developers, My python version is 2.6.3 and I would like to upgrade it to 2.7.3. So is there anything that we need to on Galaxy after Python is upgraded to a new version? Thanks, Luobin

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Job handler keeps crashing
by Derrick Lin 23 Jan '13

23 Jan '13

Hi guys, We have updated our galaxy to 20 Dec 2012 release. Recently we found that some submitted jobs could not start (stay gray forever). We found that it was caused by the job manager sent jobs to a handler (handler0) whose python process crashed and died. >From the handler log we found the last messages right before the crash: galaxy.jobs.handler DEBUG 2013-01-18 15:00:34,481 Stopping job 3032: galaxy.jobs.handler DEBUG 2013-01-18 15:00:34,481 stopping job 3032 in drmaa runner We restarted the galaxy, handler0 is up for few seconds then died again with the same error messages except the job number moved to the next one. We observed that the jobs it was trying to stop are all previous jobs whose status is either "deleted" or "deleted_new". We have never seen this in the past, so wondering if there is bugs in the new release? Cheers, Derrick

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JAVAscript error after initiating tool
by Joachim Jacob 22 Jan '13

22 Jan '13

Hi all, For who is interested. Occasionally I get this strange Javascript error, just after clicking 'run' on a tool. ERROR updating hdas from api history contents:e47699a32b93ce7f The tool gets running, but the history panel is not updated. I click 'analyse data' to see the updated history. Cheers, 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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