January 2010 - galaxy-user - lists.galaxyproject.org

setting environment for sge scripts
by Andreas Kuntzagk 15 Apr '10

15 Apr '10

Hi, I followed the advice for multiple installed python versions to set ~galaxy/galaxy-python/python and set the environment for the galaxy user to have that in the PATH Problem is, when a job is started on GridEngine, it does not use the "-V" flag to inherit the environment. So it runs with a different python version and more important it does not set LD_LIBRARY_PATH and fails for some tools which need some special lib. (libRblas in this case) Where can I fix that? regards, Andreas

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Small RNA gene, tRNA genes
by Kluger, Yuval 18 Mar '10

18 Mar '10

Hi, I would appreciate any suggestion how one can use Galaxy to obtain coordinates of human and mouse of all known tRNAs. Similarly how one can do that for other types such as miRNAs and other small RNAs . Thanks, Yuval ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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eprimer3 missing?
by Erick Antezana 29 Jan '10

29 Jan '10

Hi, I have seen that many tools from EMBOSS have already an "XML tool file" (.../tools/emboss_5/*.xml). I couldn't find the one for eprimer3 (it seems it was there before? as it could be seen in ./.hg/store/fncache : data/tools/emboss/emboss_eprimer3.xml). I have looked for it in the bitbucket but I couldn't find it... Has it ever existed? or should I create myself an XML for such tool? cheers, Erick

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Maq output
by Michaela Lee 29 Jan '10

29 Jan '10

Does anyone know if Maq can produce alignment data in SAM format? Currently we can only generate outputs in fastq format. Is there a way Galaxy can convert a fastq file to a SAM file? I did not see it as an option but I thought I'd ask. Thanks! Michaela

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pysam egg
by Erick Antezana 28 Jan '10

28 Jan '10

Hi, I've just updated my Galaxy install. Everything works fine. I only had an issue while trying to use the pysam egg. The error message is the following: ImportError: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /home/bio/erick/.python-eggs/pysam-0.1.1-py2.4-linux-x86_64.egg-tmp/pysam/csamtools.so) Unfortunately, we have in our system GLIBC 2.5 (glibc-2.5-42.el5_4.2). We have tried to bypass such requirement by compiling pysam and manually copying the csamtools.so file without success. Once I try to launch Galaxy (run.sh) it fetches the original egg (and so library)... The variable FETCH_EGGS was set to 0 but it is still fetching the latest versions...Are we missing something? Otherwise, would it be possible to have such egg for glib 2.5 ? thanks, Erick

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Re: [galaxy-user] GALAXY Question
by Guruprasad Ananda 26 Jan '10

26 Jan '10

Hi Mike, Do you mind sharing your history with me (guru(a)psu.edu) so that I can take a look at what might be going on? Thanks, Guru. > From: Michael Wilson <michael.d.wilson(a)gmail.com> > Date: January 26, 2010 12:43:30 PM EST > To: Anton Nekrutenko <anton(a)bx.psu.edu> > Subject: Re: [galaxy-user] GALAXY Question > > Dear Anton, > > I have a question regarding the 'Base Coverage' function. I have a 9 column interval file and when I perform 'Base coverage' it reports 0 bp of sequence despite there being many intervals. If I convert the same file to a bed file and then perform 'Base Coverage' I get the correct number of basepairs. There does not seem to be any problem with my interval files. I was wondering if this may be a bug. > > As I would like to use 'Base Coverage' in one of my workflows I tried to get around this problem by converting my interval files to bedfiles with 1:chrom 2:start 3:end (I do not indicate strand or name in these bedfiles). However when I use Filter and Sort: Select > ^chr21 , the new bedfile which is created with only lines starting with chr21 has for some reason had column 6 replaced with '+' and is labelled as 'strand' and column 8 is labeled with 'name'. I am not sure why the bedfile changes format after using the select command and if this is intentional or if you know a way around this happening. > > 1) can you use Base Coverage on interval files? > 2) is there a way to avoid changing the column designations in a bedfile when using Filter and Sort: select. > > > Thank you again for all your help and excellent resources. > > Best regards, > > Mike

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Re: [galaxy-user] [galaxy-bugs] workflow database
by Jeremy Goecks 25 Jan '10

25 Jan '10

Hi Jason, In the last couple weeks we've written the infrastructure that (a) enables users to publish workflows and (b) provides a way to browse, search, view, and use published workflows. (Histories and pages will have the same functionality as well.) This code is making it's way to our main webserver (it's being tested right now), and it should become available within the week. FYI, the links for published items will be: http://main.g2.bx.psu.edu/workflow/list_published http://main.g2.bx.psu.edu/history/list_published http://main.g2.bx.psu.edu/page/list_published Finally, a good place to pose these types of questions is galaxy-user, which I've CC'ed Best, J. On Jan 24, 2010, at 3:18 PM, Jason Miller wrote: > Hi I'm a user of galaxy and I was wondering if there is a database or website where users can submit workflows to be public? I know it's possible to make links or share with other users, but I thought it would be a good idea to have a database of workflows for everyone to see. > Thanks > Jason > > > > > > > > > > > > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs

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Re: [galaxy-user] alignment question
by Anton Nekrutenko 22 Jan '10

22 Jan '10

Michaela: Sorry for delay in replying. Looks like you need to do this: 1. Map reads with bowtie using "try hard" option. 2. Leave -m option at -1 3. Set -k ridiculously high (e.g., 1000) 4. Once mapped filter SAM with "SAM Tools->Filter SAM on bitwise flag" filter tool using option as in the attached image 5. Convert SAM format to intervals using "Covert SAM to interval" tool. 6. Subtract coordinates of regions from the previous step from coordinates of your exons using "Operate on Genome Intervals- >Subtract" tool. The result will contain unmapped regions. Let me know how it goes, and always cope to galaxy-user mailing list. Thanks, anton galaxy team On Jan 20, 2010, at 2:16 PM, Michaela Lee wrote: > Hi Anton, > > I am sorry to keep bothering you but could you clarify a bit more on > what I can do with mapped reads on Galaxy? Here is my situation: > We have attempted to sequence all the exons on the X chromosome for > some of our subjects through exon capture and high through-put > sequencing. We have all the Illumina reads on an external hard > drive and would like to know which regions of our reference sequence > were not "captured" or sequenced after mapping all the reads using > Maq or Bowtie. We are not interested in unmapped reads, just the > unmapped regions of the reference sequence. > > I have watched video #7 of Galaxy but I am confused as to which > "bitwise flag" I would use to have Galaxy generate an output file > with a list of regions of the reference sequence that were not > mapped. Ultimately, we would like to compare all the regions that > were not captured for all our subjects to see if those unsequenced > regions are random or not. > > I appreciate any help you can give me. Thank you! > > Michaela Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Sharing Histories, Workflows, and Pages
by Jeremy Goecks 20 Jan '10

20 Jan '10

Hi all, Changeset 3253 stabilizes Galaxy's item sharing; items that can be shared are histories, workflows, and pages. There are now three types of sharing for items: (1) sharing via email with other users (unchanged); (2) making an item accessible via link (similar to 'enable import via link'); and (3) publishing an item. Sharing via email is unchanged; you can share item with individual users by specifying their email addresses. Making an item accessible via link generates a human-readable link that can be shared with other people; via this link, users can view or import an item. Publishing an item makes the item accessible via link and lists the item's link in Galaxy's public repository so that anyone via browse or search for it. Hence, in reference to a previous discussion about item sharing, it is now possible to generate a link for accessing an item but not publish the item's link. This changeset is available now in our development repository and will make its way to our dist repository and our main server in the next week. Comments, questions, and suggestions are welcome. Thanks, J.

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alignment question
by Michaela Lee 15 Jan '10

15 Jan '10

Hello, I was wondering if Galaxy can align Solexa reads to a reference sequence. If not, can I upload my alignment data from Maq onto Galaxy and somehow work with that data online? Also, can Galaxy tell me which parts of the reference sequence have no reads aligned to them? I am basically trying to figure out which parts were not sequenced and compare those sequences between different subjects. Thanks for your help. M

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