- galaxy-dev - lists.galaxyproject.org

random_lines_two_pass.py slow
by Ido Tamir 17 Oct '13

17 Oct '13

Hi, my users start to take comparability serious and start to downsample. But it seems like the random_lines_two_pass.py tool is very slow with large input files, like bed files with 40million reads to e.g. 33million reads https://bitbucket.org/galaxy/galaxy-dist/src/2469c53051ea/tools/filters/ran… I don't understand the rationale behind the deletion of the positions from the array, in most programming languages deletion from an array is slow. Benchmarking the two random sampling methods was too difficult for me, I removed the get_random_by_subtraction method, and my users are happy. Did anybody really benchmark this? thank you very much, ido

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Interact with running job?
by Jonas Hagberg 17 Oct '13

17 Oct '13

Hej I am new to Galaxy. I am reading the documentation but could not really find an answer . I would like to create a tool that when after executed on a cluster the user should be able to interact with the running job. Get the current output and make a plot and see how far the job has come. Clicking on special status link on the running job in history or something like that. How would one do this in galaxy. Is there any way today to do it with the tools in galaxy. Would be great to get some first guidance where to start. cheers -- Jonas Hagberg BILS - Bioinformatics Infrastructure for Life Sciences - http://bils.se e-mail: jonas.hagberg(a)bils.se, jonas.hagberg(a)scilifelab.se phone: +46-(0)70 6683869 address: SciLifeLab, Box 1031, 171 21 Solna, Sweden

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Integrate Galaxy workflow as a tool in Galaxy
by shenwiyn 17 Oct '13

17 Oct '13

Hi Galaxy team, We find that Galaxy workflow is much more convenient and operable for biodata analysing.Now we get an idea about integrating our Galaxy workflow as a tool in Galaxy,such as RNAdenovo,Chip-seq,and so on.We do not know whether some other Galaxy try the same or not ,and whether it is necessary and feasible for our idea.Thank you for any suggestions. shenwiyn

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Apache and Galaxy
by UMD Bioinformatics 17 Oct '13

17 Oct '13

Hello, I have set up a galaxy instance and I'm trying to use Apache so that I can access UCSC. I have the following set in my httpd.conf (below) file in Apache2 and I've altered the folioing in my universe_wsgi.ini file. When I launch galaxy I no longer see my history. If it attempt to login the screen refreshes but it does not log me into the system. i.e. my history does not show up and I do not get the admin tab to appear. What am I doing wrong? httpd.conf settings #Changes for Galaxy 16 Oct 2013 # Define Galaxy as a valid Proxy <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> RewriteEngine on <Location "/"> XSendFile On XSendFilePath / </Location> RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/static/style/(.*) /Volumes/Jose-Drobo/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/(.*) /Volumes/Jose-Drobo/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /Volumes/Jose-Drobo/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /Volumes/Jose-Drobo/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] #ucsc <Location "/root/display_as"> Satisfy Any Order deny,allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location> <LocationMatch /ucsc_(bam|big) > # This is to enable bam and bigWig (or bigBEd in the future) by traversing the proxy # Allow from our internal network # and set the http header to a fake email address, this is required because of galaxy architecture... Satisfy any Order deny,allow Allow from all </LocationMatch> Changes to universe_wsgi.ini host = 0.0.0.0 [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy filter-with = proxy-prefix cookie_path = /galaxy apache_xsendfile = True allow_user_creation = True environment_setup_file = /Volumes/Jose-Drobo/galaxy-dist/.bashrc Cheers Ian

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Re: [galaxy-dev] [galaxy-user] Need your helps about Galaxy
by James Taylor 17 Oct '13

17 Oct '13

They are already running a local instance. I didn't realize that bowtie required a different index for colorspace alignment. So Lei, you will have to build the index using bowtie-build -C. -- James Taylor, Associate Professor, Biology/CS, Emory University On Wed, Oct 16, 2013 at 3:31 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: > Hello Lei, > > If genomes are not listed, that means that they are not indexed for use with > the tool. The test server is primarily for demonstration or test use > besides, and there could be other unexpected issues even if genomes are > listed (we really do test here). Also, the quotas are very small (10G). If > you want to use this tool, a local, cloud, or slipstream Galaxy is > recommended. Full choices with details are listed here: > http://wiki.galaxyproject.org/BigPicture/Choices > http://usegalaxy.org/toolshed > > Help for setup is here, with the galaxy-dev(a)bx.psu.edu mailing list > available for further support. Tools will need to be installed, and indexes > created. You can rsync the genome, but most genomes will not have loc file > entries and indexes for SOLiD already created - see the Tophat manual for > the command to create these: > http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uni… > http://wiki.galaxyproject.org/Admin/Data%20Integration > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup > > Hopefully this helps! > > Jen > Galaxy team > > > On 10/16/13 11:57 AM, Lei Yan wrote: >> >> Hi all, >> >> We are trying to use “Tophat for SOLiD”. >> But this tool (Tophat for SOLiD) does not seem to be linked to the >> reference genomes that are installed. I can see those genomes on the Tophat >> for illumina tool and the other tools that require a reference genome. >> Please see attachments. >> Does anybody have any ideas for this? Thanks a lot. >> >> >> Lei Yan >> Center for Integrative and Translational Genomics >> The University of Tennessee Health Science Center > > > -- > Jennifer Hillman-Jackson > http://galaxyproject.org >

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/dev/xvda1 filling up when downloading large files via ftp
by Stanislas Werfel 17 Oct '13

17 Oct '13

Dear all, this problem has been mentioned before by McDowell(a)vims.ed, but there was no solution so far posted. I'm using the current cloudman on Amazon AWS. When I download a fastq.gz file via an EBI-SRA ftp link using the "Upload File" function, although the file itself is loading to the /mnt/galaxy drive, at the same time /dev/xvda1 is filling up and at some point the download stops and says "[Errno 28] No space left on device". I've checked in the universe_wsgi.ini and the ftp upload path is set correctly to /mnt/galaxy/tmp/ftp. Here's the df output: Filesystem 1K-blocks Used Available Use% Mounted on /dev/xvda1 10321208 9797012 0 100% / udev 8736124 8 8736116 1% /dev tmpfs 3497960 232 3497728 1% /run none 5120 0 5120 0% /run/lock none 8744896 0 8744896 0% /run/shm cgroup 8744896 0 8744896 0% /sys/fs/cgroup /dev/xvdb 423135208 207440 401433728 1% /mnt /dev/xvdf 104847360 22055572 82791788 22% /mnt/galaxy /dev/xvdg 733900800 685188288 48712512 94% /mnt/galaxyIndices I'm also having another issue: when I delete files in the history in galaxy, they don't acually get deleted in the files/000/ folder. And galaxy is still showing them under "Using ..." in the total space used. So if I download a 3GB fastq file, then delete everything in the history, Using is still showing 3GB and the file is still there in the folder. Could the two issues be connected? Are there maybe some rights missing for the galaxy instance to delete files? Thanks in advance for any help Best Stanislas

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Can not find hg_g1k_v37.fa.
by shenwiyn 16 Oct '13

16 Oct '13

Hi everyone, I want to use the hg_g1k_v37.fa on my local Galaxy,but I can not find this data.When I use the command : rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/hg_g1k_v37/seq/hg_g1k_v37.fa the error occurred: receiving incremental file list rsync: link_stat "/hg_g1k_v37/seq/hg_g1k_v37.fa" (in indexes) failed: No such file or directory (2) sent 4 bytes received 6 bytes 4.00 bytes/sec total size is 0 speedup is 0.00 rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1532) [receiver=3.0.6] Please any suggestions would be most welcome. Thanks. shenwiyn

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Default values for repeat sections
by Eric Rasche 16 Oct '13

16 Oct '13

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello all, I've been digging through the available galaxy tool config files and have been unable to find a solution, so I bring my problem to you. I have the following (pretty generic) repeat section in a tool config I'm working on <repeat min="1" name="rpt_0" title="Colour Group"> <param value="EDHK" name="match" optional="False" type="text" label="String of letters that should be matched " /> <param value="red" name="fg" optional="False" type="text" label="Foreground colour for a group " /> <param value="blue" name="bg" optional="False" type="text" label="Background colour for a group " /> </repeat> However, for this particular tool, the default ought to be the repeat section three times, with different defaults each time. Is there any way to specify a repeat section, with a default of being repeated N times with an appropriate number of defaults set for each repeat? Cheers, Eric Rasche -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.19 (GNU/Linux) iQIcBAEBAgAGBQJSXgHgAAoJEMqDXdrsMcpVxUIQAM3UC3CZl//N47YPm+/Y5OVm Im2A9Y784rf6nk8Guq0wz4UOMSvnpgJnjlDew49Ly6UGgTdpZqBlbv+o0VQlk/Zz zs90TLVwQ8SMt5x4cSrEF8CJY7y4MlUDCxlaqSeGxmrH7FV3Ph+aRyfhsm32JJx0 duasl4WlJb3jtsBUhMBEQksuhIXTz8SgI0pfTnZ/EIp9ryWNRJiOqeLvCoHq0eNT othEkHmQn7G/o303fPGOcjpkM7SI+uFDtJLowSYBQeds+nIq9iYgcqeEBe7SmsUJ o9Fl4/duQ5aztx5Mg858U4y3lWRJoMwK9MxUqii9zacyepWMCrDFo7ZSyBgik5q8 RXgzr/ehifbMfPH04VaOI2rVtmQVlEQUVhok6JnG92V/Pu1tvZr9PQs5csNVl+ov 2xerZjKeUILeMkP2uOwCm4kPVlVwBW0mOMaSPEUQyFdsz/0HKV3h7RDLB7YFDcc8 DxIeHBY3mvBCd30RcniN42HZUes0bq+cg5eFej9zEwZxEinQKzEWRQFtCR+Mt+z9 4mBUE2gDO5OVL+m6iIt+k8lMevKx3cHom9say+jTNKiK1zbXfwqTda4vYYKxfQY8 1Nv/XPs1bIoFPFJJJIkQALeweENsjZ6iY0aJ5kGR4ZLRAMXVt34g5+r2PmXiphbT eZvA/INKRhwwiPBUf3Hg =RJCY -----END PGP SIGNATURE-----

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Consistently denied server access
by Rhea Datta 16 Oct '13

16 Oct '13

Hello, My account is under rrdatta.nyu(a)gmail.com. I have been able to successfully transfer files and performed FTP uploads using Filezilla in the past. However in the last few days I have been consistently denied server access. The report I get is: Status: Connection attempt failed with "ECONNREFUSED - Connection refused by server". Please let me know if you have a solution to this problem. Thank you so much Rhea -- *Rhea R Datta, PhD* Postdoctoral Associate New York University rrd5(a)nyu.edu rrdatta.nyu(a)gmail.com (917) 613 4719

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colaborativ pages
by Philippe Moncuquet 16 Oct '13

16 Oct '13

Hi, Is there any way to make collaboration on pages possible. I would like user to be able to modify an existing and publicly shared page when the creator of the page wants to offer this opportunity. It might be a bit complicated and out of the scope of Galaxy right now but I wanted to hear what you think about that ? Philip

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