Re: [galaxy-dev] unit tests failures
Hi, Thanks a lot for your answer. I've manually changed lib/galaxy/objectstore/__init__.py while waiting for the fixed to be released. All the unit tests now pass. Anne. On 23 Jan 2012, at 18:51, Nate Coraor wrote: On Jan 23, 2012, at 6:22 AM, Anne Pajon wrote: Hello, I've installed recently galaxy on one of our test server with python2.7 and I am running out of ideas on how to solve the issue related to this unit test failure: galaxy.objectstore.DiskObjectStore. Here is the output when running sh run_unit_tests.sh. Hi Anne, This has been fixed in changeset 8a597b83448f. Unfortunately, this changeset is not part of the current stable release. It will be in the next one, however. https://bitbucket.org/galaxy/galaxy-central/changeset/8a597b83448f --nate -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)7958 511 353 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ 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/
Re: [galaxy-dev] (no subject)
On 01/24/2012 06:19 AM, Vidya .H.K wrote: Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail. by simulating a complete command line I meant the following: You look how macs_wrapper.py is called by galaxy. This is written in the macs_wrapper.xml and then you execute the same command line. But I just realize, you have re-submitted the same question in a different e-mail thread again (unfortunately, again without a subject line). Thanks in advance As I wrote in my previous e-mail: Please send all follow-up with a cc to the mailing list (reply-all). In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote: Hi, Sorry for delayed reply. When I execute macs_wrapper.py on command line, I get the following error. python macs_wrapper.py File stdin, line 1 python macs_wrapper.py Thanks in advance On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/
[galaxy-dev] Fwd: Some eggs are out of date...Fetch failed (Mac OS X 10.6) ERRATA CORRIGE
ERRATA CORRIGE: sorry :( $ echo $PATH /System/Library/Frameworks/Python.framework/Versions/2.6/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin Original Message Subject: [galaxy-dev] Some eggs are out of date...Fetch failed (Mac OS X 10.6) Date: Tue, 24 Jan 2012 22:06:42 +0100 Hi, I'm pretty new to Galaxy, at least to this side. I'm sorry to bother you with my issue, that, I read, was quite extensively discussed previously, but even if I think to have followed correctly the instruction and further suggestions, I'm still not able to overcome the problem. I'm trying to install a local instance of Galaxy on my MAC (OS X10.6.8) My Python version is 2.6.1 and I just installed Mercurial 2.0.2 for MacOS X 10.6. FYI $ python --version Python 2.6.1 --- wrong ---see above $ echo $PATH /Users/myName/System/Library/Frameworks/Python.framework/Versions/2.6/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin When I try to run the run.sh I get the error attached below. Can you envisage a possible reason why I'm getting this error? Sorry for the naive admission, but from the error message I'm not even capable to understand which are the missing eggs... If I'd have ignored a previous post with the solution, I apologize in advance. Thank you a lot for your attention. Lu -- $ sh run.sh Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /Users/myName/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /Users/myName/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /Users/myName/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py, line 518, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. ___ 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/
[galaxy-dev] Uploading large file in browser
Hello, I have local instance of galaxy and wanted to modify upload file so that I will be able to upload large files ( 2GB). The reason I am trying to do this in browser is that extra tools for FTP do not really work in my environment because of all the constraints and firewalls. I came up with jQuery file upload tool (http://blueimp.github.com/jQuery-File-Upload/), and the tool seems fine if it is possible me to integrate into my galaxy instance. My questions are: -Is it too cumbersome to achieve this goal with external tools? -how deep should I hit the galaxy (at the code level) to integrate this jquery tool? -Are there any alternatives to upload large files in browser without FTP? Thanks, Daniel ___ 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/
[galaxy-dev] Error Msg: Cluster could not complete job
Dear Galaxy Support, I'm getting the following error message when trying to process larger Solid files. ERROR MESSAGE: Cluster could not complete job - Compute Quality Statistic-- First got the error message. Ran ok after re-running the job. - Subsequent job of converting qual/csfasta - fastq failed with same error message - Doesn't seem to happen on small solid files Potentially relevant information: 1. Cloud Instance on Amazon/Large instance 2. Only one master node on cluster. 3. Has been updated using the update feature to a version as of late last week. 4. Only 1 user right now on system, so there shouldn't be any competing load. 5. Downloaded a bunch of data files, so volume was at 94%. Currently in process of expanding volume. Question: Is this expected behavior or have I misconfigured something (i.e. some timeout value)? Any suggestions? Thanks in advance, Dave P.S. I'm new to galaxy and impressed so far. Keep up the great work. ___ 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/
Re: [galaxy-dev] software installs: PATH vs env.sh
Thanks for the replies. One extra element I failed to properly describe is that we are running on a cluster with a similar setup to CloudMan. This means we have a galaxyTools/tools directory with folders for each tool, and subfolders for each version with a default symlink to the version currently in use. Each subfolder has a env.sh script which is added by the dependency manager to the qsub script to be processed at runtime . I was thinking that one of the benefits of using the requirements tag is that it would/could allow for tool and version specific dependency chains. For instance if a version of tophat only runs with a certain version of bowtie but you want to make the newest beta version of bowtie also available to run independently. Right now the (sort of problem) I am having is that in order for the necessary PATH information to be transmitted to the compute nodes I have to have bowtie and samtools listed as requirements in the tool wrapper. The PATH variable of the galaxy user doesn't transmit to the compute nodes (despite having it set before launching the main instance of galaxy). With our current setup I have seen this with several different tools that call other tools and so I am wondering if my cluster/cloud setup has gone wrong somewhere. Is there a right way or place to specify the runtime PATH so that it will be transmitted to the compute nodes? Just trying to figure this out in terms of best practices since my current setup seems to require modification of the default wrappers to transmit PATH information to the compute nodes. Thanks again, Andrew On Sun, Jan 22, 2012 at 8:00 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: On 01/22/2012 01:41 AM, Anthonius deBoer wrote: All tools need to be in the path of the user running galaxy. but can be simply added to the path by adding them to the 'run.sh' script Regards, Hans Regards, Thon Thon de Boer, Ph.D Bioinformatics Guru T: +1.650.799.6839 | E-mail: thondeb...@me.com http://www.linkedin.com/pub/**thon-de-boer/1/1ba/a5bhttp://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b IMPORTANT NOTICE: This email message is legally privileged, confidential and is for the use of the individual or entity to whom it is addressed. If you have received this email message by error, please immediately notify us by email and delete the message. Thank you. On Jan 21, 2012, at 3:50 PM, Andrew Warrenanwar...@vbi.vt.edu wrote: Hello, We recently transitioned from a CloudMan instance of galaxy to our own cluster and started having problems with calls to tools from within other tools. For example when Tophat calls bowtie-inspect its not finding the executable. To fix this I listed bowtie in the requirements section of the tophat wrapper like so: tool id=tophat name=Tophat for Illumina version=1.5.0 descriptionFind splice junctions using RNA-seq data/description version_commandtophat --version/version_command requirements requirement type=packagetophat/**requirement requirement type='package'bowtie/**requirement requirement type=packagesamtools/**requirement /requirements Now I am wondering, is it generally expected that all tools used by galaxy will have their executables on the user galaxy's PATH? Is the above a good solution? Or is there something else likely amiss with our galaxy setup? I think we recently pulled updates for some major tool_shed release but I haven't been able to determine if any of the tools listed above were affected by that. Wish I were in Český Krumlov asking this question. Missed the registration deadline...doh. Thanks, Andrew Warren __**_ 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/ ___ 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/
Re: [galaxy-dev] installing MACS tool
Hi Dan, Thank you Dan. This was very helpful.I installed MACS version 1.3 and now the tool is working. Hi Vidya, One quick thing to check is that you installed MACS version 1.3 which is supported by the wrapper and not version 1.4 which is not yet supported. Thanks for using Galaxy, Dan On Jan 24, 2012, at 7:41 AM, Hans-Rudolf Hotz wrote: On 01/24/2012 06:19 AM, Vidya .H.K wrote: Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail. by simulating a complete command line I meant the following: You look how macs_wrapper.py is called by galaxy. This is written in the macs_wrapper.xml and then you execute the same command line. But I just realize, you have re-submitted the same question in a different e-mail thread again (unfortunately, again without a subject line). Thanks in advance As I wrote in my previous e-mail: Please send all follow-up with a cc to the mailing list (reply-all). In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote: Hi, Sorry for delayed reply. When I execute macs_wrapper.py on command line, I get the following error. python macs_wrapper.py File stdin, line 1 python macs_wrapper.py Thanks in advance On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/ ___ 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/
Re: [galaxy-dev] MACS installation
Hi, Thank you very much for your help. I have resolved the problem. I had install MACS version 1.3 instead of MACS version 1.4. Now the tool is working fine. On 01/24/2012 06:19 AM, Vidya .H.K wrote: Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail. by simulating a complete command line I meant the following: You look how macs_wrapper.py is called by galaxy. This is written in the macs_wrapper.xml and then you execute the same command line. But I just realize, you have re-submitted the same question in a different e-mail thread again (unfortunately, again without a subject line). Thanks in advance As I wrote in my previous e-mail: Please send all follow-up with a cc to the mailing list (reply-all). In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote: Hi, Sorry for delayed reply. When I execute macs_wrapper.py on command line, I get the following error. python macs_wrapper.py File stdin, line 1 python macs_wrapper.py Thanks in advance On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/
