galaxy-dev March 2013

galaxy-dev@lists.galaxyproject.org

108 participants
185 discussions

Uploading large data sets from cluster file system for local galaxy install
by Raj Ayyampalayam 22 Mar '13

22 Mar '13

Hello, I have a question for the many galaxy admins here. I am in the process of setting up a local galaxy install submitting the jobs as real users to our local SGE cluster. I am trying to figure out the best way to load large datasets (Sequence files etc..) stored in the local clusters storage. These files might not be world readable and we cannot assume that the user knows how to make it so. I was wondering if anybody here has tackled the problem and found a workable solution? Thanks, -Raj

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Re: [galaxy-dev] Galaxy: Dependency error htseq_count
by Lance Parsons 22 Mar '13

22 Mar '13

Glad that everything works now for you. The "Get Updates" functionality won't work since this is a new version of the tool (updated version of HTSeq package). Since the updated version could generate different results with the same input, Galaxy keeps the old version around for reproducibility reasons. I don't know why you have to restart Galaxy for the tool to show up. As far as I know, that should not be necessary, and also shouldn't be dependent on anything in the tool wrapper configuration. I'm aware of the issue with the screenshot missing. I'm not sure how to get the tool wrapper to point to the static images installed from the toolshed (or if that's even possible). In the meantime, a workaround would be to copy the count_modes.png file from the repository to the [GALAXY_HOME]/static/images directory. Lance Joachim Jacob | VIB | wrote: > *sorry for my late reply - we have experienced some email issues lately * > > Thanks, a clean install from the new versions works! > > Unfortunately, the 'get updates' from the admin interface of Galaxy > does not find any updates with the old version. > > So, I searched the main toolshed, and I was able to install the new > version next to the old (instead of updating). The install succeeded, > but I always have to restart Galaxy to get the tool available in the > toolbox. > > > One small remark: the screenshot in the tool's interface below the > parameters is not shown. > > > 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 > > On 03/11/2013 06:34 PM, Lance Parsons wrote: >> I have posted an updated version of the htseq-count tool in the >> toolshed that uses and updated version of the HTSEQ count package >> (0.5.4p1) and hopefully addresses the installation issue you have >> experienced. Please try it out and let me know if you still have >> problems. >> >> Lance >> >> Joachim Jacob | VIB | wrote: >>> Hi Lance, >>> >>> [apologies for directly emailing to you and not through the >>> galaxy-dev list. I will post it on the dev list later on] >>> >>> I am trying to install htseq-count, but it fails during the >>> dependency installation of htseq. >>> >>> The error I get is: >>> >>> error: can't create or remove files in install directory >>> >>> The following error occurred while trying to add or remove files in the >>> installation directory: >>> >>> [Errno 2] No such file or directory: >>> '/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-30482.pth' >>> >>> >>> The installation directory you specified (via --install-dir, >>> --prefix, or >>> the distutils default setting) was: >>> >>> /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/ >>> >>> This directory does not currently exist. Please create it and try >>> again, or >>> choose a different installation directory (using the -d or >>> --install-dir >>> option). >>> >>> Any idea whether it is related to my setup (and what I can do about >>> it)? Note: only the htseq_count dependency is not being installed. >>> Thanks for providing the htseq_count wrapper! Now getting it through >>> the toolshed will make it again a little closer to a perfect world :-) >>> >>> >>> 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 >>> >>> On 12/17/2012 05:28 PM, Lance Parsons wrote: >>>> Thanks for looking into this Greg. The environment where I'm >>>> having this problem is our testing and production systems. >>>> >>>> Both environments are CentOS release 5.8 (Final) with Mercurial >>>> version 2.4.1. >>>> >>>> Interestingly, when I tried the same thing with a development setup >>>> on my OSX box (10.6.8) with Mercurial 2.4 I did not have the same >>>> issue. One difference is that on my testing/production boxes I do >>>> have an older version of the tool installed, so perhaps that is the >>>> issue. >>>> >>>> I also tried uninstalling, but that led to the (expected) error >>>> that that a previous changeset is installed: >>>> The tool shed repository htseq_count with owner lparsons and >>>> changeset revision f320093f1e8e was previously installed using >>>> changeset revision 5d969cb56112. The repository has been >>>> uninstalled, however, so reinstall the original repository instead >>>> of installing it again. You can get the latest updates for the >>>> repository using the Get updates option from the repository's >>>> Repository Actions pop-up menu. Click here to manage the repository. >>>> >>>> I then attempted to reinstall and I got a javascript message the >>>> cloning failed, and the repo is now "stuck" in the cloning state. >>>> I did not see anything in the paster logs regarding this at all. >>>> >>>> >>>> Here are the steps I took on my local system: >>>> >>>> 1. Upload htseq-count v0.3 to local toolshed >>>> >>>> 2. Install on local galaxy >>>> >>>> 3. Upload htseq-count v0.3-release2 to toolshed >>>> >>>> [Errno 2] No such file or directory: >>>> '/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/database/community_files/000/repo_3/./tool_data_table_conf.xml.sample' >>>> >>>> >>>> STDOUT from paster >>>> htseq-count.xml does not exist! >>>> sam_fa_indices.loc.sample does not exist! >>>> static/images/count_modes.png does not exist! >>>> test-data/htseq-test-paired.bam does not exist! >>>> test-data/htseq-test-paired_counts.tsv does not exist! >>>> test-data/htseq-test-paired_othercounts.tsv does not exist! >>>> test-data/htseq-test.bam does not exist! >>>> test-data/htseq-test.gff does not exist! >>>> test-data/htseq-test.sam does not exist! >>>> test-data/htseq-test_counts.tsv does not exist! >>>> test-data/htseq-test_othercounts.tsv does not exist! >>>> tool_data_table_conf.xml.sample does not exist! >>>> 4. Second attempt to upload >>>> The file 'htseq-count_0.3.release2.tar.gz' has been successfully >>>> uncompressed and uploaded to the repository. 1 undesirable items >>>> (.hg .svn .git directories, .DS_Store, hgrc files, etc) were >>>> removed from the archive. 13 files were removed from the repository >>>> root. >>>> >>>> 5. Get repository updates >>>> The installed repository named 'htseq_count' has been updated to >>>> change set revision '74a6a8221337'. >>>> >>>> >>>> >>>> Greg Von Kuster wrote: >>>>> Hi Lance, >>>>> >>>>> I tried several scenarios today in an attempt to reproduce this >>>>> but I was not able to. Have you tried uninstalling the repository >>>>> (check the checkbox to completely uninstall it) and then reinstall >>>>> it? I'm trying to reproduce this on a mac running mercurial >>>>> version 2.2.3 and Python 2.5. What's your environment? >>>>> >>>>> Greg Von Kuster >>>>> >>>>> >>>>> On Dec 13, 2012, at 2:30 PM, Lance Parsons wrote: >>>>> >>>>>> Since I've had issues with workflow and the toolshed in the past, >>>>>> I have changed my workflow so that my only interaction with the >>>>>> toolshed is either via uploading a tarball via the web interface >>>>>> or installing a tool into my local Galaxy via the web interface >>>>>> (or occasionally just downloading tarballs). >>>>>> >>>>>> In this specific case, I uploaded a tar.gz file of the entire >>>>>> tool wrapper directory. I did NOT increment the tool version. >>>>>> In the past, incrementing the tool version has generally worked >>>>>> fine. However, when I leave the tool version the same, but >>>>>> change something (such as the help text for the tool), and then >>>>>> upload a tarball to the toolshed, I am unable to pull updates >>>>>> into my local galaxy instance. I get an error similar to what I >>>>>> have described. >>>>>> >>>>>> I hope this is enough information, but let me know if I can >>>>>> provide more detail, etc. I would very much like to get to the >>>>>> root of this issue, since it has plagued my attempts to use the >>>>>> toolshed smoothly when (seemingly inevitable) minor changes need >>>>>> to be made. In the past I have just had to wait until I update >>>>>> the tool version, as no changes can be made to the installed >>>>>> revision in my production Galaxy instance. >>>>>> >>>>>> Greg Von Kuster wrote: >>>>>>> Hi Lance, >>>>>>> >>>>>>> What process did you use for updating the tool shed repository >>>>>>> and how many separate repositories did you use? You should not >>>>>>> be updating a local repository, pushing the changes to the tool >>>>>>> shed repository, and then attempting to pull the changes back to >>>>>>> the same repository. Your repository environment should be >>>>>>> something like this: >>>>>>> >>>>>>> DEV REPO ( all development updates are performed here, so this >>>>>>> is where the tool version is incremented ) >>>>>>> | >>>>>>> V >>>>>>> <pushed changeset> >>>>>>> | >>>>>>> V >>>>>>> EXISTING TOOL SHED REPO >>>>>>> | >>>>>>> V >>>>>>> <pulled changeset to some previously cloned repo> >>>>>>> | >>>>>>> V >>>>>>> PREVIOUSLY CLONED (possibly production) REPO >>>>>>> >>>>>>> In other words, nothing should ever get pushed and pulled from >>>>>>> the tool shed repo into the same repo. If this is the process >>>>>>> you used, it would undoubtedly result in the behavior you saw. >>>>>>> If you used separate repos as I describe above, we'll need more >>>>>>> details as to the process you used in order to determine the >>>>>>> cause of the problem. >>>>>>> >>>>>>> Greg Von Kuster >>>>>>> >>>>>>> >>>>>>> On Dec 10, 2012, at 1:45 PM, Lance Parsons wrote: >>>>>>> >>>>>>>> I recently updated the htseq-count tool in the Galaxy toolshed >>>>>>>> to version 0.3. This version has some functional changes and >>>>>>>> thus the tool version was incremented. I installed this new >>>>>>>> version of the tool in my local Galaxy instance. >>>>>>>> >>>>>>>> However, I realized later that I missed updating one part of >>>>>>>> the help text. Today I fixed that text (but left the tool >>>>>>>> version the same), tarred up the file, and uploaded it to the >>>>>>>> toolshed. I then attempted to "Get Updates" from my local >>>>>>>> Galaxy instances for that tool got the following error: >>>>>>>> >>>>>>>> URL:http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revi… >>>>>>>> >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', >>>>>>>> line 364 in respond >>>>>>>> app_iter = self.application(environ, detect_start_response) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', >>>>>>>> line 98 in __call__ >>>>>>>> environ, self.app) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', >>>>>>>> line 539 in intercept_output >>>>>>>> app_iter = application(environ, replacement_start_response) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', >>>>>>>> line 80 in __call__ >>>>>>>> return self.application(environ, start_response) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py', >>>>>>>> line 91 in __call__ >>>>>>>> return self.app( environ, start_response ) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', >>>>>>>> line 632 in __call__ >>>>>>>> return self.application(environ, start_response) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', >>>>>>>> line 160 in __call__ >>>>>>>> body = method( trans, **kwargs ) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', >>>>>>>> line 206 in decorator >>>>>>>> return func( self, trans, *args, **kwargs ) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', >>>>>>>> line 1677 in update_to_changeset_revision >>>>>>>> update_repository( repo, latest_ctx_rev ) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util_common.py', >>>>>>>> line 1428 in update_repository >>>>>>>> rev=ctx_rev ) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py', >>>>>>>> line 5661 in update >>>>>>>> rev = scmutil.revsingle(repo, rev, rev).rev() >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', >>>>>>>> line 515 in revsingle >>>>>>>> l = revrange(repo, [revspec]) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', >>>>>>>> line 588 in revrange >>>>>>>> for r in m(repo, range(len(repo))): >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', >>>>>>>> line 1414 in mfunc >>>>>>>> return getset(repo, subset, tree) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', >>>>>>>> line 156 in getset >>>>>>>> return methods[x[0]](repo, subset, *x[1:]) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', >>>>>>>> line 171 in symbolset >>>>>>>> return stringset(repo, subset, x) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', >>>>>>>> line 161 in stringset >>>>>>>> x = repo[x].rev() >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py', >>>>>>>> line 235 in __getitem__ >>>>>>>> return context.changectx(self, changeid) >>>>>>>> File >>>>>>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py', >>>>>>>> line 103 in __init__ >>>>>>>> _("unknown revision '%s'") % changeid) >>>>>>>> RepoLookupError: unknown revision '11' >>>>>>>> >>>>>>>> >>>>>>>> I believe this is because the revision I have installed (10) is >>>>>>>> not longer considered a valid revision by the toolshed (I >>>>>>>> presume since it is an older revision of with the same tool >>>>>>>> version). >>>>>>>> >>>>>>>> Any help would be appreciated. Thanks. >>>>>>>> >>>>>>>> -- >>>>>>>> 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/ >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> Lance Parsons - Scientific Programmer >>>>>> 134 Carl C. Icahn Laboratory >>>>>> Lewis-Sigler Institute for Integrative Genomics >>>>>> Princeton University >>>>>> >>>>> >>>> >>>> -- >>>> 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/ >>> >>> ___________________________________________________________ >>> 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/ >> > -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Displaying track into UCSC
by Julien SEILER 22 Mar '13

22 Mar '13

Hi all, We have installed a local galaxy server and we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) Curiously, it works fine with my personal account but it doesn't for all other users. It also works for displaying tracks based on a public dataset for all users. Could anybody explain us what's happening ? Thanks in advance for any help, Julien

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Setting up Cloudman instance
by Iry Witham 22 Mar '13

22 Mar '13

Hi Team, I am working on setting up a Cloudman instance for a course we are preparing. I have used the link provided: http://usegalaxy.org/cloudlaunch and can get an instance running. The issues are as follow: 1. I need to add tools and have not found a clear method in doing so utilizing the galaxy toolshed. 2. Once I have the instance setup and shut it down I cannot restart it cleanly. On restart it appears that nginx fails to launch since port 80 is not listening. I have not found a way to start it manually. 3. I have followed both the above provided url to setup an instance and the instructions at http://wiki.galaxyproject.org/CloudMan and have had the same results. I have read a few posts of similar issues, but have not found a solution. Any suggestions will be helpful. Thanks, Iry Witham __________________________________ Scientific Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham(a)jax.org The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Composite Datatype (auto_primary_file) not uploading
by Christos Kannas 22 Mar '13

22 Mar '13

Dear all, We have a modified Galaxy server with tools for virtual screening. You can access is at http://lisis.cs.ucy.ac.cy. We created a composite datatype (auto_primary_file) to handle PDBQT files for proteins and their config file requested by AutoDock Vina, in simple words is a composite datatype consisted of two files, a pdbqt file and a text file. We have the following problems: 1. Uploading the files needed to create such a composite datatype via the Upload Tool, stacks in upload phase, as shown in the following figure http://prntscr.com/xbosn 1. As you can see in the figure, uploading individual files works 2. In this figure http://prntscr.com/xbp6k you can see the upload options for this composite datatype. 2. Uploading composite datatypes within a data library does not provide the same functionality as the Upload Tool. Regarding problem 1 what do you think is the underlying problem? Following is the source code of this composite datatype class: class PDBQT_Protein(Html): """PDBQT Protein files, ASCII protein information files.""" MetadataElement(name = "base_name", desc = "Base name for all transformed versions of this PDBQT protein dataset", default = 'protein', readonly = False, set_in_upload = True) composite_type = 'auto_primary_file' allow_datatype_change = False file_ext = 'pdbqt_protein' def __init__(self, **kwd): Text.__init__(self, **kwd) self.add_composite_file('%s.pdbqt', description = 'PDBQT Protein File', substitute_name_with_metadata = 'base_name', mimetype = 'text/plain', is_binary = False) self.add_composite_file('%s_config.txt', description = 'PDBQT Config File', substitute_name_with_metadata = 'base_name', mimetype = 'text/plain', is_binary = False) def generate_primary_file(self, dataset = None): if dataset.metadata.base_name == "protein" and \ dataset.metadata.base_name != dataset.name: dataset.metadata.base_name = dataset.name rval = ['<html><head><title>PDBQT Protein Galaxy/LiSIs Composite Dataset</title></head>'] rval.append('<body><div>This %s composite dataset is composed of the following files:<ul>' % (dataset.metadata.base_name)) for composite_name, composite_file in self.get_composite_files(dataset = dataset).iteritems(): fn = composite_name opt_text = '' if composite_file.optional: opt_text = ' (optional)' if composite_file.get('description'): rval.append('<li><a href="%s">%s (%s)</a>%s</li>' % (fn, fn, composite_file.get('description'), opt_text)) else: rval.append('<li><a href="%s">%s</a>%s</li>' % (fn, fn, opt_text)) rval.append('</ul></div></body></html>') return "\n".join(rval) def regenerate_primary_file(self, dataset): """ cannot do this until we are setting metadata """ bn = dataset.metadata.base_name efp = dataset.extra_files_path flist = os.listdir(efp) rval = ['<html><head><title>PDBQT Protein Galaxy/LiSIs Composite Dataset</title></head>'] rval.append('<body><div>This %s composite dataset is composed of the following files:<ul>' % (bn)) for i, fname in enumerate(flist): sfname = os.path.split(fname)[-1] rval.append('<li><a href="%s">%s</a></li>' % (sfname, sfname)) rval.append('</ul></div></body></html>') f = file(dataset.file_name, 'w') f.write("\n".join(rval)) f.write('\n') f.close() def set_meta(self, dataset, **kwd): """ Set metadata... """ Text.set_meta(self, dataset, **kwd) if dataset.metadata.base_name == "protein" and \ dataset.metadata.base_name != dataset.name: dataset.metadata.base_name = dataset.name log.debug('@@@ PDBQT_Protein set_meta changed dataset.metadata.base_name to: %s' % (dataset.metadata.base_name)) if kwd.get('overwrite') == False: log.debug('@@@ PDBQT_Protein set_meta called with overwrite = False') return True try: efp = dataset.extra_files_path except: log.debug('@@@ PDBQT_Protein set_meta failed %s - dataset %s has no extra_files_path ?' % (sys.exc_info()[0], dataset.name)) return False try: flist = os.listdir(efp) except: log.debug('@@@ PDBQT_Protein set_meta failed %s - dataset %s has no extra_files_path ?' % (sys.exc_info()[0], dataset.name)) return False if len(flist) == 0: log.debug('@@@ PDBQT_Protein set_meta failed - %s extra_files_path %s is empty?' % (dataset.name, efp)) return False self.regenerate_primary_file(dataset) if not dataset.info: dataset.info = 'Galaxy/LiSIs %s PDBQT Protein datatype object' % (dataset.metadata.base_name) if not dataset.blurb: dataset.blurb = 'Composite file - %s PDBQT Protein Galaxy/LiSIs datatype' % (dataset.metadata.base_name) return True Thanks in advance, Christos -- Christos Kannas Researcher Ph.D Student e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/> kannas.christos(a)ucy.ac.cy kannas.christos(a)cs.ucy.ac.cy chriskannas(a)gmail.com Mob: (+357) 99530608

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Cannot update Cloudman from a clean install on EC2?
by Brian Lin 21 Mar '13

21 Mar '13

Hi guys, I'm running into a problem with updating a completely squeaky clean fresh cloudman install using the current ami-da58aab3 Once it is up and running, I have SSHed in and made sure the sample files in run.sh are complete. I hit the update button, and 3 or 4 minutes later when the daemon tries to restart, I get status= error. Is anyone else having this issue?? The only threads and posts I have found are from a year ago, and the line is in my run.sh. The ultimate goal of all this was just so that I could have a cufflinks version that is not 0.5. Thanks for any help anyone can provide. Brian Here are the logs: paster.log: /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * python path is: /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.5.0-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Paste-1.7.5.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loading references to tool sheds from tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded reference to tool shed: Galaxy main tool shed tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2013-03-15 02:47:27,556 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2013-03-15 02:47:27,633 At database version 114 tool_shed.galaxy_install.migrate.check DEBUG 2013-03-15 02:47:27,643 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 37, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 54, in __init__ verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/mnt/galaxyTools/galaxy-central/lib/tool_shed/galaxy_install/migrate/check.py", line 145, in verify_tools raise Exception( msg ) Exception: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Console Log: - 02:46:56 - Removing 'Galaxy' service - 02:46:56 - Shutting down Galaxy... - 02:47:25 - Starting Galaxy... - 02:47:25 - Galaxy service state changed from 'Shut down' to 'Starting' - 02:47:26 - Saved file 'persistent_data.yaml' to bucket 'cm-5b0fce1cf71e5f439fc17473dd4dcd1d' - 02:48:28 - Galaxy daemon not running. - 02:48:28 - Galaxy service state changed from 'Starting' to 'Error' - 02:48:29 - Saved file 'persistent_data.yaml' to bucket 'cm-5b0fce1cf71e5f439fc17473dd4dcd1d' - 02:49:30 - Galaxy daemon not running. pgSQL.log: LOG: database system was shut down at 2013-03-15 02:11:48 UTC LOG: autovacuum launcher started LOG: database system is ready to accept connections ERROR: relation "page_revision" does not exist STATEMENT: ALTER TABLE page ADD CONSTRAINT page_latest_revision_id_fk FOREIGN KEY(latest_revision_id) REFERENCES page_revision (id) ERROR: relation "visualization_revision" does not exist STATEMENT: ALTER TABLE visualization ADD CONSTRAINT visualization_latest_revision_id_fk FOREIGN KEY(latest_revision_id) REFERENCES visualization_revision (id) LOG: unexpected EOF on client connection SGE log: 03/15/2013 01:12:20| main|ip-10-149-20-174|I|read job database with 0 entries in 0 seconds 03/15/2013 01:12:20| main|ip-10-149-20-174|E|error opening file "/opt/sge/default/common/./sched_configuration" for reading: No such file or directory 03/15/2013 01:12:20| main|ip-10-149-20-174|E|error opening file "/opt/sge/default/spool/qmaster/./sharetree" for reading: No such file or directory 03/15/2013 01:12:20| main|ip-10-149-20-174|I|qmaster hard descriptor limit is set to 8192 03/15/2013 01:12:20| main|ip-10-149-20-174|I|qmaster soft descriptor limit is set to 8192 03/15/2013 01:12:20| main|ip-10-149-20-174|I|qmaster will use max. 8172 file descriptors for communication 03/15/2013 01:12:20| main|ip-10-149-20-174|I|qmaster will accept max. 99 dynamic event clients 03/15/2013 01:12:20| main|ip-10-149-20-174|I|starting up GE 6.2u5 (lx24-amd64) 03/15/2013 01:12:20| main|ip-10-149-20-174|W|can't open job sequence number file "jobseqnum": for reading: No such file or directory -- guessing next number 03/15/2013 01:12:20| main|ip-10-149-20-174|W|can't open ar sequence number file "arseqnum": for reading: No such file or directory -- guessing next number 03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost "ip-10-149-20-174.ec2.internal" already exists 03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost "ip-10-149-20-174.ec2.internal" already exists 03/15/2013 02:46:57|listen|ip-10-149-20-174|E|commlib error: got read error (closing "ip-10-149-20-174.ec2.internal/drmaa/416") -- Brian Lin contact(a)brian-lin.com brian.lin(a)tufts.edu

2 3

workflow parameters
by Langhorst, Brad 21 Mar '13

21 Mar '13

Workflow parameters still seem to be broken for me. I'm seeing the same problem as Liisa Koski http://dev.list.galaxyproject.org/Can-t-specify-workflow-parameters-for-int… (this message comes up when i edit a workflow with ${mininsert} set on a bowtie2 job) Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save. * Step 9: Bowtie2 * Value no longer valid for 'Minimum insert size for valid paired-end alignments', replaced with default but Im running a release release_2013.02.08 and I've verified that this commit is present in the running code https://bitbucket.org/galaxy/galaxy-central/commits/73bb36c4ee3b34c3ca32ed8… any ideas? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

2 3

Cloudman on openstack
by Zeeshan Ali Shah 21 Mar '13

21 Mar '13

Hi, any update for cloudman with openstack . the page seems quite old http://wiki.galaxyproject.org/CloudMan/OpenStack -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah

2 1

customtrack visualisation
by Shaun Webb 21 Mar '13

21 Mar '13

Hi, I have lost my view in UCSC link on my customtrack datatypes, I'm not sure when this happened. External display links are still working ok for other datatypes. I have set the genome database to hg18. Any idea what I will need to edit to get this back? Thanks Shaun webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

3 3

Problems with rsync from datacache.g2.bx.psu.edu/indexes
by Rodolfo Aramayo 20 Mar '13

20 Mar '13

Hi, I hope this is the right place to ask, I am trying to rsync from: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ and I am getting the error: @ERROR: chroot failed rsync error: error starting client-server protocol (code 5) at main.c(1534) [Receiver=3.0.9 I know I can rsync to any other places Do you happen to know what is going on? Thanks --Rodolfo

3 2

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galaxy-dev March 2013