- galaxy-user - lists.galaxyproject.org

GCC2012 Registration Deadline
by Dave Clements 17 Jul '12

17 Jul '12

Hello all, This is the final email reminder that the registration deadline for the 2012 Galaxy Community Conference, is at Midnight, Central US time, on Wednesday, July 18. If you aren't registered by the end of Wednesday, you will pay *double* using late/on-site registration. The deadline for booking hotel rooms at the discounted rate has been extended until July 23, or until they fill up (and it looks like they will fill up). The 2012 conference already has more content and more participants than any previous Galaxy meeting. We would love to have you join us. See http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> for details and links. Thanks, Dave C -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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UCSC tools
by i b 17 Jul '12

17 Jul '12

Hi, is there a way to create a jobin my history from UCSC genome browser that contains ONLY genes encoding for ONLY cell surface proteins? How can I do that? Thanks a lot! ngs-ib

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(no subject)
by i b 17 Jul '12

17 Jul '12

ok, so if I have 3 different samples I would use 3 different goups and add my samples as replicate within each group. or did you mean to create just one group and add all my 3 samples as 3 replicates within that only group? thanks a lot ngs-ib ________________________________________ From: Jennifer Jackson [jen(a)bx.psu.edu] Sent: Tuesday, July 17, 2012 1:58 AM To: Irene Bassano Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] cuffdiff Hello Irene, On 7/16/12 4:11 PM, Irene Bassano wrote: > Hi, > just few questions about cuffdiff if anyone can answer: > > 1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two files Change the tool form for the option "Perform replicate analysis:" to be "Yes" (the default is "No"). Use two conditions (Groups). > > 2.what to use as input: cufflinks, cuffcompare or cuffmerge? GTF output from any of these may be appropriate. Please see the tutorial on Galaxy main at: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise FAQ: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq And the "Common uses" protocols on the Cufflinks web site plus their new paper (also linked at this site, from side bar, as "Protocol"): http://cufflinks.cbcb.umd.edu/tutorial.html Best, Jen Galaxy team > > > Thanks a lot! > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > -- Jennifer Jackson http://galaxyproject.org

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cuffdiff
by Irene Bassano 16 Jul '12

16 Jul '12

Hi, just few questions about cuffdiff if anyone can answer: 1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two files 2.what to use as input: cufflinks, cuffcompare or cuffmerge? Thanks a lot!

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galaaxy history size (gb)
by Irene Bassano 16 Jul '12

16 Jul '12

Hi, I deleted several jobs from my history (and purged history as well), however the used space on history hasn't changed. What is the limit of Gb that can e stored?Can this be updated when files are deleted permanently? Thanks, ib

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cufflinks reference annotation
by Irene Bassano 16 Jul '12

16 Jul '12

HI guys, how do we know when to select a refernce annotation when running cufflinks?And if yes, which one from UCSC should we chose: refgene or knowngenes? Thanks, ib

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sharing and publishing workflows using myExperiment
by David De Roure 16 Jul '12

16 Jul '12

We are pleased to announce a new facility in Galaxy for sharing and publishing Galaxy workflows via the myExperiment social website, which is the leading social website for scientific workflow sharing. myExperiment can now be accessed easily while you're using the Galaxy servers - you can export your workflows to myExperiment to store and share them, and import Galaxy workflows from myExperiment. This means you can: - Share Galaxy workflows in a controlled way (e.g. within a project), publish them with a stable myExperiment reference for your papers (which is linked-data compatible), and use myExperiment's discovery facilities to find more Galaxy workflows as content grows. - Use the social website features directly to document, tag and discuss workflows, add licensing, credit and attribution, and to bundle your Galaxy workflows with associated data, documents, presentations etc into myExperiment "packs" for ease of reuse and preservation. - Benefit from a central workflow website with a broad community, which means you can manage workflows for multiple Galaxy installations, attract visitors to your workflows and research, and network with others. Instructions are below and in more detail on http://wiki.myexperiment.org/index.php/Galaxy_Help This new facility is brought to you by a myExperiment-Galaxy collaboration and will increase in value as more Galaxy workflows are uploaded so we encourage you to do so - we hope you find it useful and we welcome feedback (contact details are on the help page). Best regards -- Dave 1. When using Galaxy you can import Galaxy workflows from myExperiment by choosing "Upload or import workflow" in Galaxy's workflow menu, then the new "Visit myExperiment" link at the bottom of the page. Within the myExperiment interface you can then view a Galaxy workflow and select "Import this workflow into Galaxy". Some Galaxy tutorial workflows are currently available to help you try this out. 2. To export Galaxy workflows to myExperiment you'll first need a myExperiment username and password, then you'll be able to upload Galaxy workflows and also make them visible to others if you wish. To create a username and password go to http://www.myexperiment.org/ and register. Having a username and password enables you to benefit from all the features of the site. 3. To export a Galaxy workflow to myExperiment select "Download or Export" from Galaxy's workflow menu, enter your myExperiment username and password in the "Export to myExperiment" section and click the "Export" button. Exported workflows are set to be "Private" by default but you can make them visible publicly or to friends, groups etc by clicking on "Click here to view the workflow on myExperiment" and changing the Sharing settings. 4. Visit http://www.myexperiment.org/ at any time to change settings, add further description, tags, license etc, and to create "packs". You can also create and administer groups, link up with friends and network with other workflow users.

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Generating pile-up files without spliced (intronic) regions.
by Mohammad Heydarian 15 Jul '12

15 Jul '12

Hello, Is there a way to generate a pile-up from a BAM file in SAMtools without including spliced (intronic) regions? Alternatively, is there a way to split spliced reads in a BAM file? Thanks in advance! Cheers, Mo Heydarian

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account
by Victoria Spartacus 15 Jul '12

15 Jul '12

Hello, I want to use Galaxy today but I can't. Galaxy told me that all my account has been marked deleted and I need to contact to Galaxy administrator to restore my accounts. Could you restore my accounts because I have been started some huge calculus and very important. Thank's of everything. Best regards, Victoria Spartacus

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Re: [galaxy-user] Trackster error: indexing
by Jeremy Goecks 14 Jul '12

14 Jul '12

Hi Nancy, I'm ccing the galaxy-user mailing list as this discussion may be helpful to others. The problem is that your BAM dataset isn't sorted. Galaxy requires that uploaded BAMs be sorted to be useful for most tools and for visualization. You can fix this in two ways: (a) using samtools from the command line and then uploading the sorted file to Galaxy: samtools sort in.bam out_prefix (b) from Galaxy, use tools to convert the BAM to SAM and back again to BAM; the output of the SAM to BAM tool will be sorted. Taking either of these steps will enable visualization in Trackster. Best, J. On Jul 13, 2012, at 5:34 PM, Nancy Au Yeung wrote: > > On Fri, Jul 13, 2012 at 2:29 PM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: > Hi Nancy, > > Can you share the history with the problematic dataset(s) with me and I can take a look? Please share the history with me using my email address: jeremy.goecks(a)emory.edu > > Best, > J. > > On Jul 12, 2012, at 9:07 PM, Nancy Au Yeung wrote: > >> Hi, >> >> I saw another post regarding trackster error and it seems like this is different. I have tried copying the dataset from the History option, but this same error occurs. See error script below. >> >> Thanks! >> >> Trackster Error >> >> *** glibc detected *** python: double free or corruption (top): 0x0000000001c09370 *** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x75ab6)[0x7f93fe421ab6] >> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f93fe4267ec] >> /lib/x86_64-linux-gnu/libc.so.6(fclose+0x14d)[0x7f93fe412a0d] >> /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7f93fdac2ad7] >> /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x6e7f8)[0x7f93fdaae7f8] >> python(PyObject_Call+0x36)[0x4824c6] >> python(PyEval_CallObjectWithKeywords+0x36)[0x486086] >> /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x52a04)[0x7f93fda92a04] >> python[0x482068] >> python(PyObject_Call+0x36)[0x4824c6] >> python(PyEval_EvalFrameEx+0x91a)[0x4c5e8a] >> python(PyEval_EvalCodeEx+0x136)[0x4ccee6] >> python(PyEval_EvalFrameEx+0x838)[0x4c5da8] >> python(PyEval_EvalCodeEx+0x136)[0x4ccee6] >> python(PyRun_FileExFlags+0xe1)[0x577901] >> python(PyRun_SimpleFileExFlags+0x177)[0x577b37] >> python(Py_Main+0x6f7)[0x550497] >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)[0x7f93fe3caead] >> python[0x41dea1] >> ======= Memory map: ======== >> 00400000-00672000 r-xp 00000000 fe:00 893421 /usr/bin/python2.7 >> 00871000-00872000 r--p 00271000 fe:00 893421 /usr/bin/python2.7 >> 00872000-008db000 rw-p 00272000 fe:00 893421 /usr/bin/python2.7 >> 008db000-008ed000 rw-p 00000000 00:00 0 >> 0166d000-01c29000 rw-p 00000000 00:00 0 [heap] >> 7f93f8000000-7f93f8021000 rw-p 00000000 00:00 0 >> 7f93f8021000-7f93fc000000 ---p 00000000 00:00 0 >> 7f93fd6de000-7f93fd70e000 r-xp 00000000 00:18 458639 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/ctabix.so >> 7f93fd70e000-7f93fd80d000 ---p 00030000 00:18 458639 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/ctabix.so >> 7f93fd80d000-7f93fd812000 rw-p 0002f000 00:18 458639 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/ctabix.so >> 7f93fd812000-7f93fd814000 rw-p 00000000 00:00 0 >> 7f93fd814000-7f93fd83b000 r-xp 00000000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so >> 7f93fd83b000-7f93fda3a000 ---p 00027000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so >> 7f93fda3a000-7f93fda3b000 r--p 00026000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so >> 7f93fda3b000-7f93fda3f000 rw-p 00027000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so >> 7f93fda3f000-7f93fda40000 rw-p 00000000 00:00 0 >> 7f93fda40000-7f93fdb10000 r-xp 00000000 00:18 458638 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so >> 7f93fdb10000-7f93fdc10000 ---p 000d0000 00:18 458638 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so >> 7f93fdc10000-7f93fdc20000 rw-p 000d0000 00:18 458638 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so >> 7f93fdc20000-7f93fdc25000 rw-p 00000000 00:00 0 >> 7f93fdc25000-7f93fdc44000 r-xp 00000000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so >> 7f93fdc44000-7f93fde44000 ---p 0001f000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so >> 7f93fde44000-7f93fde45000 r--p 0001f000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so >> 7f93fde45000-7f93fde4e000 rw-p 00020000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so >> 7f93fde4e000-7f93fdf0f000 rw-p 00000000 00:00 0 >> 7f93fdf0f000-7f93fdf12000 r-xp 00000000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so >> 7f93fdf12000-7f93fe111000 ---p 00003000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so >> 7f93fe111000-7f93fe112000 r--p 00002000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so >> 7f93fe112000-7f93fe114000 rw-p 00003000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so >> 7f93fe114000-7f93fe196000 rw-p 00000000 00:00 0 >> 7f93fe196000-7f93fe1ab000 r-xp 00000000 fe:00 122656 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f93fe1ab000-7f93fe3ab000 ---p 00015000 fe:00 122656 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f93fe3ab000-7f93fe3ac000 rw-p 00015000 fe:00 122656 /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f93fe3ac000-7f93fe529000 r-xp 00000000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so >> 7f93fe529000-7f93fe729000 ---p 0017d000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so >> 7f93fe729000-7f93fe72d000 r--p 0017d000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so >> 7f93fe72d000-7f93fe72e000 rw-p 00181000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so >> 7f93fe72e000-7f93fe733000 rw-p 00000000 00:00 0 >> 7f93fe733000-7f93fe7b4000 r-xp 00000000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so >> 7f93fe7b4000-7f93fe9b3000 ---p 00081000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so >> 7f93fe9b3000-7f93fe9b4000 r--p 00080000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so >> 7f93fe9b4000-7f93fe9b5000 rw-p 00081000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so >> 7f93fe9b5000-7f93fe9cb000 r-xp 00000000 fe:00 909634 /usr/lib/x86_64-linux-gnu/libz.so.1.2.6 >> 7f93fe9cb000-7f93febca000 ---p 00016000 fe:00 909634 /usr/lib/x86_64-linux-gnu/libz.so.1.2.6 >> 7f93febca000-7f93febcb000 rw-p 00015000 fe:00 909634 /usr/lib/x86_64-linux-gnu/libz.so.1.2.6 >> 7f93febcb000-7f93fed68000 r-xp 00000000 fe:00 909753 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 >> 7f93fed68000-7f93fef67000 ---p 0019d000 fe:00 909753 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 >> 7f93fef67000-7f93fef8d000 rw-p 0019c000 fe:00 909753 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 >> 7f93fef8d000-7f93fef91000 rw-p 00000000 00:00 0 >> 7f93fef91000-7f93fefdc000 r-xp 00000000 fe:00 909754 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 >> 7f93fefdc000-7f93ff1db000 ---p 0004b000 fe:00 909754 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 >> 7f93ff1db000-7f93ff1e3000 rw-p 0004a000 fe:00 909754 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 >> 7f93ff1e3000-7f93ff1e5000 r-xp 00000000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so >> 7f93ff1e5000-7f93ff3e4000 ---p 00002000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so >> 7f93ff3e4000-7f93ff3e5000 r--p 00001000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so >> 7f93ff3e5000-7f93ff3e6000 rw-p 00002000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so >> 7f93ff3e6000-7f93ff3e8000 r-xp 00000000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so >> 7f93ff3e8000-7f93ff5e8000 ---p 00002000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so >> 7f93ff5e8000-7f93ff5e9000 r--p 00002000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so >> 7f93ff5e9000-7f93ff5ea000 rw-p 00003000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so >> 7f93ff5ea000-7f93ff601000 r-xp 00000000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so >> 7f93ff601000-7f93ff800000 ---p 00017000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so >> 7f93ff800000-7f93ff801000 r--p 00016000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so >> 7f93ff801000-7f93ff802000 rw-p 00017000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so >> 7f93ff802000-7f93ff806000 rw-p 00000000 00:00 0 >> 7f93ff806000-7f93ff825000 r-xp 00000000 fe:00 131420 /lib/x86_64-linux-gnu/ld-2.13.so >> 7f93ff859000-7f93ff95d000 rw-p 00000000 00:00 0 >> 7f93ff98f000-7f93ffa17000 rw-p 00000000 00:00 0 >> 7f93ffa21000-7f93ffa22000 rw-p 00000000 00:00 0 >> 7f93ffa22000-7f93ffa23000 rwxp 00000000 00:00 0 >> 7f93ffa23000-7f93ffa25000 rw-p 00000000 00:00 0 >> 7f93ffa25000-7f93ffa26000 r--p 0001f000 fe:00 131420 /lib/x86_64-linux-gnu/ld-2.13.so >> 7f93ffa26000-7f93ffa27000 rw-p 00020000 fe:00 131420 /lib/x86_64-linux-gnu/ld-2.13.so >> 7f93ffa27000-7f93ffa28000 rw-p 00000000 00:00 0 >> 7fff744fb000-7fff7451c000 rw-p 00000000 00:00 0 [stack] >> 7fff74589000-7fff7458a000 r-xp 00000000 00:00 0 [vdso] >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] >> Aborted >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ > >

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