galaxy-dev January 2012

galaxy-dev@lists.galaxyproject.org

88 participants
161 discussions

How to define comment character for output files
by Sabry Razick 04 Jan '12

04 Jan '12

Hello, 1. How to define a character used at the beginning of a comment for ourput file. i.e. if "#" is used at the start of the comment Galaxy recognises this, but what if I want to use some other character. is it possible to define this inside <outputs> ? <outputs> <data name="output" format="custom_format" label="${input.name}_mappedreads.yyy"> </data>  </outputs> 2. How does the "Number of comment lines" populated in the file properties ? (form where does Galaxy get this information from when the "auto detect button is pressed" ?) Regards, Sabry.

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Problem with uploading SMALL file to Galaxy on EC2 and get "client intended to send too large body"
by Thon deBoer 04 Jan '12

04 Jan '12

I am trying to setup a instance of Galaxy on the EC2 cloud and everything seems to be going OK. Everything installs correctly and I can start Galaxy with no problems. But when I try to upload a SMALL BAM file (~5 MB), it just hangs there and never completes... When I look at the error.log I see the following error message: 2011/12/09 19:27:32 [error] 929#0: *1204 client intended to send too large body: 4719398 bytes, client: 173.195.189.92, server: localhost, request: "POST /tool_runner/index HTTP/1.1", host: "ec2-50-17-113-5.compute-1.amazonaws.com", referrer: "http://ec2-50-17-113-5.compute-1.amazonaws.com/tool_runner?tool_id=upload1" It seems to have a problem with the size of the body... Anyone have an idea how to fix this? I am using ami-da58aab3 Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer(a)me.com LinkedIn Profile

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tool_type="data_source_async"
by Matt Vincent 04 Jan '12

04 Jan '12

Hello all, I am trying to configure an Asynchronous tool (I can get it to work synchronously). My configuration looks something like this for the tool: <?xml version="1.0"?> <tool name="mytoolname" id="myunique_tool_id_1" tool_type="data_source_async"> <description>mytool description</description> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://myurl" check_values="false" method="post"> <display>Go to MyTool $GALAXY_URL</display> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> <request_param galaxy_name="URL" remote_name="URL" missing="" /> <request_param galaxy_name="jobname" remote_name="jobname" missing="N/A" /> </request_param_translation> <uihints minwidth="800"/> <outputs> <data name="output" format="zip" /> </outputs> <options sanitize="False" refresh="True"/> </tool> This works fine and downloads the data, but I was expecting Galaxy to post another GALAXY_URL parameter for me to generate the data and than post back to Galaxy once done. This is described here... http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources However, I never receive “another” GALAXY_URL as descripbed in Step 1 of the Asynchronous data depositing section. I am using the most recent version of Galaxy. Can someone please show an example? Matt

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Galaxy tool's error report
by Timothy Wu 04 Jan '12

04 Jan '12

Hi, I'm executing a R script via Python's os.system() (using Rscript executable which allow executing R script in the command line). This script makes use of library that will attempt to load up Tcl/Tk interface. Though I don't see anything even if I'm running the commands on Windows interactive R console, it will attempt to connect to the display server unsuccessfully during Galaxy's execution (and fail because $DISPLAY is not set). The program runs just fine since I have the output I wanted. But Galaxy sees error, and I'm suspecting it's because of this DISPLAY thing. I don't understand how Galaxy detects something goes wrong. If anything I thought it's my Python script return code that should matter. But how does Galaxy know?! And how do I fix it? Timothy

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Problem with the output of megablast
by Sandrine Hughes 04 Jan '12

04 Jan '12

Dear all, I’m using the online version of Galaxy (I’m just a user, not a developer) and I think that there might be a problem with the output of Megablast. Indeed, I’ve noticed that the GI of the database hit (given column 2 in the output table) is not in agreement with the details given in the other columns (notably the length of the hit is inaccurate). After some investigation (see below for all the details), I think that in most cases, the problem comes from a shift of –1 between the GI number and the details associated. Can you confirm that there is a problem ? Do you think that it will possible to fix it ? Many thanks for you help as we really need this step in our process of analysis, Sandrine Here are the details: I. First, what I have done : I used the program to identify the species that I have in a mix of unknown sequences by using the following options: Database nt 27-Jun-2011 Word size 16 Identity 90.0 Cutoff 0.001 Filter out low complexity regions Yes I run the analyses twice and obtained exactly the same results (I used the online version of Galaxy, not a local one). II. Second, I analysed the data obtained for one of my sequence (1-202). The following lines are the beginning of the table that I obtained after the megablast and two lines with troubles: 1-202 312182292 484 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 312182201 476 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 308228725 928 99.33 150 1 0 1 150 19 168 2e-75 289.0 1-202 308228711 938 99.33 150 1 0 1 150 22 171 2e-75 289.0 1-202 308197083 459 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392378 920 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392376 918 99.33 150 1 0 1 150 9 158 2e-75 289.0 1-202 300392375 922 99.33 150 1 0 1 150 11 160 2e-75 289.0 1-202 300392374 931 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392373 909 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392371 1172 99.33 150 1 0 1 150 9 158 2e-75 289.0 ... 1-202 179366399 151762 98.67 150 2 0 1 150 46880 47029 6e-73 281.0 1-202 58617849 511 98.67 150 2 0 1 150 21 170 6e-73 281.0 III. Third, what I’ve noticed: My first trouble was that among all the species identified, two were very different from the expected ones (2 last lines). So I decided to search if that could be possible for that sequence and performed independently a megablast on the NCBI with similar options. I was not able to find these two species in the results. So, I decided to check the hits identified in the table above and identified a second trouble. In the table, the second column give the GI of the database hit and the third column give the length of the database hit. However, when I manually checked in NCBI the length of the GI, this one was incorrect. Indeed, for the GI 312182292, the length should be 580 and not 484. By checking different lines, I noticed that the length that is given for a GI corresponds to the length of the GI-1. As you can see in the above table, some GI are consecutive (300392376, 300392375,...). When checking the length of 300392376 in NCBI, I should have 920. But when I checked 300392375, I found 918. And this was true for the following lines : 300392374 give normally 922 and 300392373 give 931... My conclusion at that point was that there was a shift of –1 between the GI and the other parameters of the line (indeed the parameters for the remaining columns are in agreement with the length of the GI-1). However, that’s not always true.... For some GI given in the table (for example, the two last lines), if we check the parameters of the GI-1, the parameters are completely different... So, I suppose that there is a trouble in the GI sorting during the megablast but I’m not able to clearly define the problem. IV. Fourth, confirmed with an other dataset In order to be sure that the problem was not linked to my data or my process, I asked a colleague to do a megablast on independent data. The conclusions were similar to mine : a shift in the GI given in the table and the parameters associated, that most of the time but not always, correspond to GI-1.

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04 Jan '12

Hi all - I had this problem once before with a previous installation, and thought it was fixed, but I'm seeing it again and not sure its related. I have Galaxy running with a Proxy server on apache to get /galaxy instead of using port 8080. I've disabled load balancing and running everything in one process. I've set up the admin user using: admin_users = myemail(a)mydomain.edu then restarted Galaxy. I was already logged in, refreshed the page, and didn't see the Admin page, so I logged out. I tried to log back in but get redirected to the main galaxy page and I'm still not logged in. I checked the galaxy logs and see the following: serving on 0.0.0.0:8080 view at http://127.0.0.1:8080 galaxy.web.framework DEBUG 2012-01-03 16:18:29,994 Error: this request returned None from get_history(): http://bic/galaxy/ 10.24.51.101 - - [03/Jan/2012:16:18:29 -0400] "GET /galaxy/ HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7" 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] "GET /galaxy/root/tool_menu HTTP/1.1" 200 - "http://bic/galaxy/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7" 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] "GET /galaxy/history HTTP/1.1" 200 - "http://bic/galaxy/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7" galaxy.web.framework DEBUG 2012-01-03 16:18:30,594 Error: this request returned None from get_history(): http://bic/galaxy/root/user_get_usage 10.24.51.101 - - [03/Jan/2012:16:18:30 -0400] "POST /galaxy/root/user_get_usage HTTP/1.1" 500 - "http://bic/galaxy/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7" Error - <type 'exceptions.AssertionError'>: Could not determine anonymous user's history. URL: http://bic/galaxy/root/user_get_usage File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 67 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 203 in user_get_usage return self.__user_get_usage( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/root.py', line 206 in __user_get_usage usage = trans.app.quota_agent.get_usage( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/quota/__init__.py', line 29 in get_usage assert history, "Could not determine anonymous user's history." AssertionError: Could not determine anonymous user's history. CGI Variables ------------- CONTENT_LENGTH: '-1' HTTP_ACCEPT: 'application/json, text/javascript, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a60ab36dc18d043e05577a892e93c9dadb26d3a1556c8c957dfed888be5af1bfd; galaxysession=c6ca0ddb55be603a1703b65966de4e010d7a3dd39f711df6d65d3ab9d5876cfd9280ce1808870f14' HTTP_HOST: 'bic' HTTP_ORIGIN: 'http://bic' HTTP_REFERER: 'http://bic/galaxy/history' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_2) AppleWebKit/534.52.7 (KHTML, like Gecko) Version/5.1.2 Safari/534.52.7' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/root/user_get_usage' REMOTE_ADDR: '10.24.51.101' REQUEST_METHOD: 'POST' SCRIPT_NAME: '/galaxy' SERVER_NAME: 'bic.cag.chop.edu' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' Configuration ------------- __file__: '/home/galaxy/galaxy-dist/universe_wsgi.ini' admin_users: 'golharr(a)gmail.com' apache_xsendfile: 'True' cookie_path: '/galaxy' database_connection: 'postgres:///galaxy' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' debug: 'False' default_cluster_job_runner: 'pbs:///' enable_pages: 'True' here: '/home/galaxy/galaxy-dist' new_file_path: '/home/galaxy/galaxy-dist/database/tmp' nglims_config_file: 'tool-data/nglims.yaml' set_metadata_externally: 'True' start_job_runners: 'pbs' static_cache_time: '360' static_dir: '/home/galaxy/galaxy-dist/static/' static_enabled: 'True' static_favicon_dir: '/home/galaxy/galaxy-dist/static/favicon.ico' static_images_dir: '/home/galaxy/galaxy-dist/static/images' static_scripts_dir: '/home/galaxy/galaxy-dist/static/scripts/' static_style_dir: '/home/galaxy/galaxy-dist/static/june_2007_style/blue' use_interactive: 'False' use_nglims: 'False' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x1ae5cf10> paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a1703b65966de4e010d7a3dd39f711df6d65d3ab9d5876cfd9280ce1808870f14'>, 'galaxysession=c6ca0ddb55be603a60ab36dc18d043e05577a892e93c9dadb26d3a1556c8c957dfed888be5af1bfd; galaxysession=c6ca0ddb55be603a1703b65966de4e010d7a3dd39f711df6d65d3ab9d5876cfd9280ce1808870f14') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x1ae5cd50> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x16b60990> paste.recursive.forward: <paste.recursive.Forwarder from /galaxy> paste.recursive.include: <paste.recursive.Includer from /galaxy> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /galaxy> paste.recursive.script_name: '/galaxy' paste.throw_errors: True webob._parsed_post_vars: (MultiDict([]), <FakeCGIBody at 1b856fd0 viewing MultiDict([])>) webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------ First, I'm not sure that's normal. It doesn't seem to be related, because it happens even if I bring up a new Galaxy page. I can't log in as a user as well. There is no error in the galaxy log file so I'm not sure how to track this one down.

1 2

Torque / scrambling pbs_python
by Ryan Golhar 04 Jan '12

04 Jan '12

Hi - I've just finished installing a ROCKS 5.4.3 cluster and am now adding Galaxy to it. We are using torque instead of SGE. I see the Wiki docs at http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster state I need to scramble pbs_python by doing: LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python I have libtorque installed in /usr/lib64: [galaxy@bic x86_64]$ ll /usr/lib64/libtorque.* -rw-r--r-- 1 root root 536862 Dec 28 12:32 /usr/lib64/libtorque.a -rwxr-xr-x 1 root root 810 Dec 28 12:32 /usr/lib64/libtorque.la lrwxrwxrwx 1 root root 18 Dec 28 13:50 /usr/lib64/libtorque.so -> libtorque.so.2.0.0 lrwxrwxrwx 1 root root 14 Dec 28 13:50 /usr/lib64/libtorque.so.0 -> libtorque.so.2 lrwxrwxrwx 1 root root 18 Dec 28 13:50 /usr/lib64/libtorque.so.2 -> libtorque.so.2.0.0 -rwxr-xr-x 1 root root 766431 Dec 28 12:32 /usr/lib64/libtorque.so.2.0.0 So I then run (and get the error shown at the bottom): [galaxy@bic x86_64]$ cd [galaxy@bic ~]$ cd galaxy-dist/ [galaxy@bic galaxy-dist]$ LIBTORQUE_DIR=/usr/lib64/libtorque.so.2.0.0 python scripts/scramble.py -e pbs_python fetch_one(): Trying to fetch: http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz fetch_one(): Fetched to: /home/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.1.0.tar.gz unpack_source(): Unpacked to: /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python copy_build_script(): Using build script /home/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python: /share/apps/Python-2.6.7/bin/python scramble.py --------------------------------------------------------------------------- This script requires setuptools version 0.6c11 to run (even to display help). I will attempt to download it for you (from http://pypi.python.org/packages/2.6/s/setuptools/), but you may need to enable firewall access for this script first. I will start the download in 8 seconds. (Note: if this machine does not have network access, please obtain the file http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg and place it in this directory before rerunning this script.) --------------------------------------------------------------------------- Downloading http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg checking for pbs-config... /usr/bin/pbs-config Found torque version: 2.5.9 checking for python... /share/apps/Python-2.6.7/bin/python checking for python version... 2.6 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.6/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages configure: creating ./config.status config.status: creating Makefile config.status: creating setup.py scramble(): Patching setup.py running egg_info creating src/pbs_python.egg-info writing src/pbs_python.egg-info/PKG-INFO writing top-level names to src/pbs_python.egg-info/top_level.txt writing dependency_links to src/pbs_python.egg-info/dependency_links.txt writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' reading manifest file 'src/pbs_python.egg-info/SOURCES.txt' writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' running bdist_egg installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib.linux-x86_64-2.6 copying src/pbs.py -> build/lib.linux-x86_64-2.6 copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6 running build_ext building '_pbs' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DTORQUE_2_4 -I/share/apps/Python-2.6.7/include/python2.6 -c src/pbs_wrap.c -o build/temp.linux-x86_64-2.6/src/pbs_wrap.o src/pbs_wrap.c:2622: warning: function declaration isn't a prototype src/pbs_wrap.c:2630: warning: function declaration isn't a prototype gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o -L/usr/lib64 -ltorque -o build/lib.linux-x86_64-2.6/_pbs.so creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg copying build/lib.linux-x86_64-2.6/pbs.py -> build/bdist.linux-x86_64/egg copying build/lib.linux-x86_64-2.6/PBSQuery.py -> build/bdist.linux-x86_64/egg copying build/lib.linux-x86_64-2.6/_pbs.so -> build/bdist.linux-x86_64/egg byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc creating stub loader for _pbs.so byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying src/pbs_python.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying src/pbs_python.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying src/pbs_python.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying src/pbs_python.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt zip_safe flag not set; analyzing archive contents... creating dist creating 'dist/pbs_python-4.1.0-py2.6-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in scramble raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) ) galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pbs_python did not appear to fail, but no egg found to copy from expected path: /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python/dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs2.egg [galaxy@bic galaxy-dist]$ cd scripts/scramble [galaxy@bic scramble]$ ll total 20 drwxrwxr-x 2 galaxy galaxy 4096 Dec 29 16:21 archives drwxrwxr-x 3 galaxy galaxy 4096 Dec 29 16:21 build drwxrwxr-x 2 galaxy galaxy 4096 Dec 29 16:22 lib drwxrwxr-x 7 galaxy galaxy 4096 Dec 29 13:25 patches drwxrwxr-x 2 galaxy galaxy 4096 Dec 29 13:25 scripts [galaxy@bic scramble]$ cd build/ [galaxy@bic build]$ ll total 4 drwxrwxr-x 3 galaxy galaxy 4096 Dec 29 16:21 py2.6-linux-x86_64-ucs2 [galaxy@bic build]$ cd py2.6-linux-x86_64-ucs2/ [galaxy@bic py2.6-linux-x86_64-ucs2]$ ll total 4 drwx------ 7 galaxy galaxy 4096 Dec 29 16:22 pbs_python [galaxy@bic py2.6-linux-x86_64-ucs2]$ cd pbs_python/dist/ [galaxy@bic dist]$ ll total 180 -rw-rw-r-- 1 galaxy galaxy 178869 Dec 29 16:22 pbs_python-4.1.0-py2.6-linux-x86_64.egg I see the egg is created, but not with the name expected by galaxy. How do I fix this?

3 3

unpacking zip files during upload
by Langhorst, Brad 03 Jan '12

03 Jan '12

I'm working on unpacking a zip file into multiple datasets. I think this is the code path Upload.py UploadToolAction upload_common.py: get_uploaded_datesets new_upload new_history_upload or new_library_upload Then a job gets spooled Which calles add_file in data_source/upload.py And does the expansion of the zip I can unpack the zip and create files in the dataset's path there. But I don't know how to create more dataset associations, and I'm not sure that it makes sense to create datasets on the fly in data_source/upload.py . Should I pass some information along with data_source/upload.py about how to create dataset object and associate them with library/history associations? Or maybe I can pass in some kind of a callback that can handle the dataset expansion? (I'm pretty new to python, but it seems similar to ruby) I thought about a composite dataset, but that seems like overloading that concept. Really the files I'm thinking about uplaoding are 8 independent BAMs or fastqs or whatever – not a set of files that are related to each other. Any suggestions? Brad -- Brad Langhorst New England Biolabs langhorst(a)neb.com

2 1

Problem uploading file by an URL
by Marc Bras 03 Jan '12

03 Jan '12

Hi, We have a Galaxy server in production and I have a problem when I want to download a huge file with HTTP URL. Galaxy starts well to download my file, but Galaxy writes this file in "/ tmp" directory. Is it possible to change this directory ? Thank you, Regards, Marc Bras -- Marc Bras ------------------------------------------ Marc.Bras(a)versailles.inra.fr INRA-URGI: Unité de Recherche Génomique Info Centre de Recherche de Versailles-Grignon Route de Saint Cyr 78026 Versailles - FRANCE Tel: +33 1 30 83 34 70 ------------------------------------------

2 1

Re: [galaxy-dev] Galaxy with PBS runner Setting
by Nate Coraor 03 Jan '12

03 Jan '12

On Dec 20, 2011, at 12:19 AM, Le-Shin Wu wrote: > Thanks a million, Nate. I was able to submit my PBS job though galaxy. But I got another problem once the PBS job is finished. > > I submit a bowtie alignment testing job to our cluster by using PBS runner through galaxy. But I always got an error message showing on the right history panel as below. > > An error occurred running this job: > # reads processed: 17214026 > # reads with at least one reported alignment: 16405756 (95.30%) > # reads that failed to align: 808270 (4.70%) > Reported 16405756 alignments to 1 output stream(s) > > In fact, the message showing here is the output message from bowtie application and I did get the correct alignment result stored on galaxy server machine. Therefore, I tried adding some PBS options, such as "-k eo" or "-j eo -o /dev/null", to the PBS runner in universe_wsgi.ini to remove the standard output message from bowtie. But this time I got the following error message. Hi Le-Shin, I am not familiar enough with bowtie to know why this error occurred. Perhaps someone else on the list can reply with some information. Please keep replies on the mailing list to ensure this is possible. > An error occurred running this job:Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. > > It looks like if galaxy PBS runner did not receive the standard output from cluster, it will throw an error. Could you please help us to solve this problem. Thanks a lot. That's correct, Galaxy controls the location of the stdout/stderr files, changing these will cause such failures. --nate > > Le-Shin > > >

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galaxy-dev January 2012