Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster
Hi, I'm having the same issue, has it been fixed since then? Thanks, L-A Le 07/11/2011 21:43, Nate Coraor a écrit : On Nov 4, 2011, at 1:11 PM, Carlos Borroto wrote: Hi, Reading a little more about this problem, I see Galaxy uses python tempfile library (http://docs.python.org/library/tempfile.html), specifically at line 70 in tools/samtools/sam_to_bam.py: tmp_dir = tempfile.mkdtemp() mkdtemp should honor TMPDIR, TEMP or TMP environment variables, I setup all tree of them in ~/.bashrc with no results. I'm using: default_cluster_job_runner = drmaa://-q all.q -V/ With -V I was hoping to be able to export all my environment variables, which seems to work for everything else, but not for the TMP. I ended hardcoding the dir argument, which is not good workaround, as I'm guessing this is not the only tool that will run into this problem: tmp_dir = tempfile.mkdtemp( dir='/home/cborroto/galaxy_dist/database/tmp') Any advice? In a more SGE related question, is there a way for me to debug what environment I'm getting when running Galaxy jobs? Hi Carlos, Try submitting an SGE job from the command line and having a look at the environment variables set on the execution host. Most likely, SGE is setting its own TMPDIR variable which would be overriding the value set with -V. --nate Thanks, Carlos On Fri, Nov 4, 2011 at 11:22 AM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi Jen, Thanks for the quick response. The workaround you describe could work, but I might run into trouble later on. My interest is to develop a workflow for GATK, which have very strict requirements on the input BAM file. One of which is that the sorting have to be exactly the same as the reference. My reference is not sorted lexicographically chr1, chr10, chr11, , but instead is sorted karyotypically chr1, chr2, I don't think I'll be able to do this with Filter and Sort - Sort. Also GATK needs the header for the @RG tags, which I could resolve by just reintroducing the header later on, but still it will be cumbersome. I'll work on my galaxy/cluster configuration and see if I can find why the SAM-to-BAM tool is failing. Thanks again, Carlos On Thu, Nov 3, 2011 at 6:35 PM, Jennifer Jacksonj...@bx.psu.edu wrote: Hello Carlos, If what you want is a sorted SAM file, then the tool Filter and Sort - Sort may be a better choice. A SAM file is a tabular file. If there is header data at the beginning of the SAM file, it can be removed before running Sort with the tool Filter and Sort - Select (with a not matching regex). Although, you can choose to not include header output as a BWA option. Perhaps this will solve the immediate problem? Best, Jen Galaxy team On 11/3/11 12:43 PM, Carlos Borroto wrote: Hi, I'm running into this error: Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_), When using SAM-to-BAM tool on a locally install Galaxy using a SGE cluster. I'm using the last version of galaxy-dist. I'm guessing I have a problem with the configuration for the tmp folder. I have this on universe_wsgi.ini: # Temporary files are stored in this directory. new_file_path = /home/cborroto/galaxy_dist/database/tmp But I don't see this directory being used and from the error looks like /tmp in the node is used. I wonder if this is the problem, as I don't know if there is enough space in the local /tmp directory at the nodes? I ran the same tool in a subset of the same SAM file and it ran fine. Also, I see this in the description of the tool: This tool uses the SAMTools toolkit to produce an indexed BAM file based on a sorted input SAM file. But what I actually need is to sort a SAM file output from bwa, I haven't found any other way than to converting it to BAM. Looking at sam_to_bam.py I see the BAM file will also be sorted. Would it be wrong to feed an unsorted SAM file into this tool? Finally, just to be sure there is nothing wrong with the initial SAM file, I ran samtools view ... and samtools sort ... on this file manually outside of Galaxy and it ran fine. Thanks in advance, Carlos ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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] galaxy-dev#64;lists.bx.psu.edu
hello this will give you a happier new year http://invest-cnbc.com/news/ talk to you soon ___ 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] GATK tools
Hi Rob, At this time, these tools are still included within the main Galaxy distribution under tools/gatk. I would recommend using the latest version available from galaxy-central until they are migrated into the toolshed. Please let us know if you encounter any issues. Thanks for using Galaxy, Dan On Apr 10, 2012, at 11:36 AM, Robert Chase wrote: Hello, One of our users has been using the GATK (beta) tools on the main instance of galaxy and would like to have them locally accessible. I have looked at the main toolshed but I couldn't find them there. Is there a place I can download the GATK files and xml files? -Rob ___ 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] param type=select and multiple=true
Hi everyone. I'm trying to use a param type=select display=checkboxes
multiple=true in a tool, but galaxy doesn't seem to work correctly if I
unselect all.
This is what I have:
param name=test type=select display=checkboxes multiple=true
label=A test
option value=a selected=trueA/option
option value=b selected=trueB/option
option value=cC/option
/param
If I unselect all, execute the tool, and then try to re-run the tool by
examining the output dataset, parameter A and B are selected, but they
shouldn't! When the history is converted to a workflow this breaks the intent
of the user!
Second problem: how do I test for single values in the command template?
Right now I'm (wrongly?) doing:
#if 'a' in $test.value:
...
#end if
but it breaks badly when all values are unselected ($test.value does not
exist, and thus cheetah fails to compile the template).
My solution would be:
#set $foo = str($test).split(',')
#if 'a' in $foo:
#end if
but this is _incredibly_ ugly. When I use a multi-select, I often want to see
if there's some single parameter in it. Any suggestions?
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[galaxy-dev] Installation issue...
Hello, I am trying to install Galaxy on Linux. I ran the sh run.sh command and was greeted with the following error: File /install_folder/galaxy-dist/lib/galaxy/datatypes/registry.py, line 146 finally: ^ SyntaxError: invalid syntax I am using Python version 2.7.1 and was hoping that anyone who has seen this before might be able to assist me. Thank you very much in advance for your help. Greg -- Dr. Gregory Miles Bioinformatics Specialist Cancer Institute of New Jersey @ UMDNJ Office: (732) 235 8817 ___ 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] delete data library via API
Hi guys, Is that possible to delete datasets in a shared data library via API? Of course when the modify permission is granted. We see delete.py in the API script folder but can't figure out how to get it work. Thanks! Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nlhttps://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_meiMobile: +31 6 41709231 ___ 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] Creating a workflow of workflows
Hi again, I'm trying to set up a workflow for Galaxy (6799:40f1816d6857), but I can't seem to find a way to make a workflow that invokes another workflow. It seems like this wouldn't be unreasonable, since workflows have defined inputs and outputs. There might be another way to accomplish what I'm trying to ultimately do, though. We have a set of analyses and conversions, and want to assemble a workflow that goes through a long series of steps. The workflow can roughly be organized into three parts. Once the workflow is finished, we might want to rerun the third or second and third parts after modifiying some of the intermediate files. It seems like this might also be accomplished by somehow marking that some input files should be substituted instead of using the outputs of some of the steps in the workflow. Anyway, I've been unable to find a simple way of doing this.. I could make each part of the workflow a tool, but if I also wanted to expose the tools used in each part, I would be duplicating those invocations and increasing the maintenance burden. I could also make separate workflows for parts 1+2+3, 2+3, and 3, but that would also be duplicating work and increasing the maintenance burden. I could also make this three completely separate workflows, but that would mean that the user would have to remember to run each of these separately. Each part can take a very long time, so it would be useful to have this set up so that a user can start from the first part on a Friday and have the output from the third part available on Monday. Thanks in advance for any help, ~Aaron ___ 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/
