galaxy-dev March 2017

galaxy-dev@lists.galaxyproject.org

36 participants
45 discussions

deprecated 'page' tag in tool xml - more than deprecated?
by Hans-Rudolf Hotz 28 Mar '17

28 Mar '17

Dear All As part of our move to upgrade from v. 16.04 to 17.01, I have noticed that the 'page' tag in the tool xml file doesn't work anymore. I know, the 'page' tag has been deprecated for a while, however, we have many old but important tools where the 'page' tag is in use. Has the functionality been removed intentionally? Though, I cant find any comments in the release notes for 16.07,16.10, and 17,01. Or is there a trick to re-enable it? Thank you very much for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Re: [galaxy-dev] Problem with downloading datasets using wget or curl
by Ashok Varadharajan 28 Mar '17

28 Mar '17

Dear Team, Can anyone help us to solve the below issue? Our galaxy users could not download large sequencing data using wget or curl. *Thanks and Regards,* *Ashok Varadharajan* On Wed, Mar 22, 2017 at 10:15 AM, Ashok Varadharajan <ashvark(a)gmail.com> wrote: > Dear Team, > > We are running galaxy-16.07 behind the proxy using nginx, uwsgi and > supervisor in scientific linux 7. I have problem with downloading > datasets using wget. > > I am getting the following html for all my datasets in the galaxy when I > try to download it using wget [for example: wget http:// > {GALAXYURL}/galaxy/datasets/xxxxxxxxxxxx/display?to_ext=tabular] > > Can anyone help me to solve this issue ? > > > <!DOCTYPE HTML> > <html> >  > <head> > <meta http-equiv="Content-Type" content="text/html; charset=utf-8" > /> > <meta name="viewport" content="maximum-scale=1.0"> > <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1"> > <title>Galaxy</title> > <link rel="index" href="/galaxy/"/> > <link href="/galaxy/static/style/jquery.rating.css?v=1489572328" > media="screen" rel="stylesheet" type="text/css" /> > <link href="/galaxy/static/style/jquery-ui/smoothness/jquery-ui.css?v=1489572328" > media="screen" rel="stylesheet" type="text/css" /> > <link href="/galaxy/static/style/base.css?v=1489572328" media="screen" > rel="stylesheet" type="text/css" /> > <link href="/galaxy/static/style/bootstrap-tour.css?v=1489572328" > media="screen" rel="stylesheet" type="text/css" /> > <script type="text/javascript"> > // this is needed *before* the app code is loaded - many MVC > access Galaxy.root for their url > // TODO: change this by using a common Backbone.Model base class > and url fn > window.Galaxy = { root: '/galaxy/' }; > </script> > </head> > <body scroll="no" class="full-content"> > <div id="everything" style="position: absolute; top: 0; left: 0; > width: 100%; height: 100%;"> > <div id="background"></div> > <div id="masthead" class="navbar navbar-fixed-top > navbar-inverse"></div> > <div id="messagebox" style="display: none;"></div> > <div id="inactivebox" class="panel-warning-message" > style="display: none;"></div> > </div> > <div id='dd-helper' style="display: none;"></div> > <noscript> > <div class="overlay overlay-background noscript-overlay"> > <div> > <h3 class="title">Javascript Required for Galaxy</h3> > <div> > The Galaxy analysis interface requires a browser with > Javascript enabled.<br> > Please enable Javascript and refresh this page. > </div> > </div> > </div> > </noscript> > <script src="/galaxy/static/scripts/bundled/libs.bundled.js?v=1489572328" > type="text/javascript"></script> > <script src="/galaxy/static/scripts/bundled/login.bundled.js?v=1489572328" > type="text/javascript"></script> > <script type="text/javascript"> > app( > {"redirect": "/galaxy/datasets/xxxxxxxxxxxxxxxx/display", > "show_welcome_with_login": false, "user": {"quota_percent": null, "id": > null, "total_disk_usage": 0.0, "nice_total_disk_usage": "0 bytes"}, > "openid_providers": [], "root": "/galaxy/", "config": > {"communication_server_host": "http://localhost", "ftp_upload_site": > null, "mailing_lists": "https://wiki.galaxyproject.org/MailingLists", > "nginx_upload_path": "/galaxy/api/tools", "terms_url": null, > "enable_unique_workflow_defaults": false, "wiki_url": " > https://wiki.galaxyproject.org/", "version_major": "16.07", > "support_url": "https://wiki.galaxyproject.org/Support", > "persistent_communication_rooms": [], "remote_user_logout_href": null, > "message_box_content": null, "logo_src": "/galaxy/static/images/galaxyIcon_noText.png", > "biostar_url_redirect": "http://{GALAXY_URL}/galaxy/biostar/biostar_redirect", > "message_box_visible": false, "ftp_upload_dir": "{ftp_upload_dir}", > "logo_url": "/galaxy/", "brand": "{BRAND}", "search_url": " > http://galaxyproject.org/search/usegalaxy/", "screencasts_url": null, > "ga_code": null, "require_login": true, "communication_server_port": 7070, > "lims_doc_url": "https://usegalaxy.org/u/rkchak/p/sts", > "inactivity_box_content": "Your account has not been activated yet. Feel > free to browse around and see what's available, but you won't be able to > upload data or run jobs until you have verified your email address.", > "citation_url": "https://wiki.galaxyproject.org/CitingGalaxy", > "allow_user_creation": false, "is_admin_user": false, > "allow_user_dataset_purge": true, "server_startttime": 1489572328, > "biostar_url": null, "datatypes_disable_auto": false, "use_remote_user": > null, "message_box_class": "info"}, "welcome_url": "/galaxy/root/welcome"}, > {} > ); > </script> > </body> > </html> > > > *Thanks and Regards,* > *Ashok Varadharajan* >

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Dataset Generation Errors
by Lapointe, David 27 Mar '17

27 Mar '17

I have installed the metaphlan tool ( dannon e951f9d38339) which installed with the dependancies seemingly satisfied. I am getting an error "This tool was disabled before the job completed" I can't determine why this happens. In the handler log is this: Tool 'toolshed.g2.bx.psu.edu/repos/dannon/metaphlan/metaphlan/1.7.0' removed from tool config, unable to run job David -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research Technology (RT) Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144 Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.edu

2 4

Convert BED to Feature Location Index breaks when "preserve_python_environment = legacy_only"
by Hans-Rudolf Hotz 27 Mar '17

27 Mar '17

Hi All I am in the process of updating our local galaxy servers to release 17.01. Using the new release, I get the following error, when I try to display a simple bed file in trackster: Traceback (most recent call last): File "/***/galaxy_dev/***/galaxy/lib/galaxy/datatypes/converters/interval_to_fli.py", line 20, in from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFReaderWrapper, read_unordered_gtf ImportError: No module named galaxy.datatypes.util.gff_util When change 'preserve_python_environment = legacy_only' to 'preserve_python_environment = always' in "galaxy.ini" it works. Looks like more tools need to be added to the "whitelist" ? Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Contributing to Galaxy project
by maximilian_greil＠web.de 26 Mar '17

26 Mar '17

3 2

Adding Custom Button Based on Eventual Output Datatype and/or Tool Used
by Joseph Brent Greer 22 Mar '17

22 Mar '17

Hi All, We'd like to add a custom button to the history panel that allows us display job progress in the middle panel. Is it possible to add a custom button that is only available for jobs that will output a specific datatype, but is available for use before the job has completed and the output has been created? Is it possible to add a custom button that is only available for specific tools? In the past we added a custom button that was modeled after the "View Details" button. That button allowed us display search progress information while the job was being processed and before the output was generated. Unfortunately, the button was added to all jobs regardless of the datatype of their eventual output. Any guidance/advice would be great. Thanks, Joe Greer

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proftpd sftp setup doesn't work
by Rui Wang 22 Mar '17

22 Mar '17

Hi Folks, I'm trying to set up the ftp for the local galaxy instance. I got the regular ftp working, but not the sftp. After a few hours attempts, I'm wondering what I'm missing. Here is the related info: 1. Configure the build install_user=bioinfoadmin install_group=bioinfoadmin ./configure --prefix=/media/libraryfiles/proftpd --enable-openssl --with-modules=mod_sql:mod_sql_postgres:mod_sql_passwd --with-modules=mod_sftp:mod_tls make make install 2. Start the server sudo sbin/proftpd --config /media/libraryfiles/proftpd/etc/proftpd.conf -n -d 10 I notice that even though I start it using sudo, the real user that is running proftpd is 'nobody'. 3. Config file snippet, I inserted the following piece to the original config file, Add 'VirtualHost' or no doesn't change anything in result <IfModule mod_sftp.c> SFTPEngine on Port 2222 SFTPLog /var/log/proftpd/sftp.log AuthOrder mod_auth_unix.c mod_sql.c # Configure both the RSA and DSA host keys, using the same host key # files that OpenSSH uses. SFTPHostKey /etc/ssh/ssh_host_rsa_key SFTPHostKey /etc/ssh/ssh_host_dsa_key #SFTPAuthMethods publickey SFTPAuthMethods password # Enable compression SFTPCompression delayed </IfModule> Now when I start the server, and then when I try to test the login, I got this: $ sftp -P 2222 localhost packet_write_wait: Connection to 127.0.0.1 port 2222: Broken pipe Couldn't read packet: Connection reset by peer Accordingly, I got the following segfault in log: 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65: ROOT PRIVS at main.c:1227 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65: RELINQUISH PRIVS at main.c:1231 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65: no matching vhost found for 127.0.0.1#2222, using 'ProFTPD Default Installation' listening on wildcard address 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ROOT PRIVS at main.c:1034 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): SETUP PRIVS at main.c:1039 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): session requested from client in unknown class 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): performing module session initializations 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): mod_cap/1.1: adding CAP_SETUID and CAP_SETGID capabilities 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ROOT PRIVS at mod_sftp.c:1674 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): RELINQUISH PRIVS at mod_sftp.c:1677 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ROOT PRIVS at keys.c:2001 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): RELINQUISH PRIVS at keys.c:2008 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ROOT PRIVS at keys.c:703 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): RELINQUISH PRIVS at keys.c:710 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ROOT PRIVS at keys.c:703 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): RELINQUISH PRIVS at keys.c:710 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ROOT PRIVS at keys.c:2001 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): RELINQUISH PRIVS at keys.c:2008 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): mod_sql/4.3: defaulting to 'postgres' backend 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): mod_ident/1.0: ident lookup disabled 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ROOT PRIVS at mod_delay.c:1756 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): RELINQUISH PRIVS at mod_delay.c:1759 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ROOT PRIVS at mod_auth.c:140 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): opening scoreboard '/media/libraryfiles/proftpd/var/proftpd.scoreboard' 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): RELINQUISH PRIVS at mod_auth.c:142 2017-03-22 00:51:14,786 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): AuthOrder in effect, resetting auth module order 2017-03-22 00:51:14,787 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): connected - local : 127.0.0.1:2222 2017-03-22 00:51:14,787 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): connected - remote : 127.0.0.1:58014 2017-03-22 00:51:14,787 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): SSH2 session opened. 2017-03-22 00:51:14,787 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): dispatching LOG_CMD command 'KEXINIT' to mod_sql 2017-03-22 00:51:14,787 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): dispatching LOG_CMD command 'KEXINIT' to mod_log 2017-03-22 00:51:14,787 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): dispatching LOG_CMD command 'ECDH_INIT' to mod_sql 2017-03-22 00:51:14,787 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): dispatching LOG_CMD command 'ECDH_INIT' to mod_log 2017-03-22 00:51:14,789 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ProFTPD terminating (signal 11) 2017-03-22 00:51:14,789 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): ProFTPD terminating (signal 11) 2017-03-22 00:51:14,789 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): mod_sftp/0.9.9: scrubbing 2 passphrases from memory 2017-03-22 00:51:14,789 cal-hsl-65 proftpd[56922] cal-hsl-65 (localhost[127.0.0.1]): SSH2 session closed. Seems that it is connected in the middle... And the /var/log/proftpd/sftp.log shows things like(many identical snippets, I just picked one randomly): 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: sent server version 'SSH-2.0-mod_sftp/0.9.9' 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: received client version 'SSH-2.0-OpenSSH_7.2p2 Ubuntu-4ubuntu2.1' 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: handling connection from SSH2 client 'OpenSSH_7.2p2 Ubuntu-4ubuntu2.1' 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: + Session key exchange: ecdh-sha2-nistp256 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: + Session server hostkey: ssh-rsa 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: + Session client-to-server encryption: aes128-ctr 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: + Session server-to-client encryption: aes128-ctr 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: + Session client-to-server MAC: umac-64(a)openssh.com 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: + Session server-to-client MAC: umac-64(a)openssh.com 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: + Session client-to-server compression: none 2017-03-22 01:16:06,753 mod_sftp/0.9.9[58288]: + Session server-to-client compression: none The version of proftpd is 1.3.5d on ubuntu 16.04.2. Not sure if anyone has seen this before. Any input will be greatly appreciated. Thanks, Rui

2 3

tabular to bed
by Matthias Bernt 22 Mar '17

22 Mar '17

Dear galaxy-devs, What would be the galaxy way to convert tabular data (e.g. the tabular output of BLAST or infernal) into bed or alignments? For bed it seems like that cutting the columns and using awk to adapt the positions to the bed definitions and switch coordinates for the reverse strand matches would do the job. But, in particular using awk seems to be "end user incompatible" :) What would be the best idea: Provide a workflow or a tool doing the job? Initially I had hoped that I can simply change the data type to bed and assign the columns in the attributes tab (but I forgot about the coordinate adjustments). Anyway there has been a problem: Then the preview in the history shows that the columns are assigned (except for the score column). It looks like this: 1.Chrom 2 3.Name 4 5 6 7 8.Start 9.End 10.Strand 11 12 13 14 15 16 17 18 But in "Show Data" the columns are still taken as is, e.g. 2nd column is start ... When I try to use the File in BedTools Merge it fails with the message that it is not a bed file. Thanks for all the help. Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Problem with downloading datasets using wget or curl
by Ashok Varadharajan 22 Mar '17

22 Mar '17

Dear Team, We are running galaxy-16.07 behind the proxy using nginx, uwsgi and supervisor in scientific linux 7. I have problem with downloading datasets using wget. I am getting the following html for all my datasets in the galaxy when I try to download it using wget [for example: wget http:// {GALAXYURL}/galaxy/datasets/xxxxxxxxxxxx/display?to_ext=tabular] Can anyone help me to solve this issue ? <!DOCTYPE HTML> <html>  <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="viewport" content="maximum-scale=1.0"> <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1"> <title>Galaxy</title> <link rel="index" href="/galaxy/"/> <link href="/galaxy/static/style/jquery.rating.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" /> <link href="/galaxy/static/style/jquery-ui/smoothness/jquery-ui.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" /> <link href="/galaxy/static/style/base.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" /> <link href="/galaxy/static/style/bootstrap-tour.css?v=1489572328" media="screen" rel="stylesheet" type="text/css" /> <script type="text/javascript"> // this is needed *before* the app code is loaded - many MVC access Galaxy.root for their url // TODO: change this by using a common Backbone.Model base class and url fn window.Galaxy = { root: '/galaxy/' }; </script> </head> <body scroll="no" class="full-content"> <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"> <div id="background"></div> <div id="masthead" class="navbar navbar-fixed-top navbar-inverse"></div> <div id="messagebox" style="display: none;"></div> <div id="inactivebox" class="panel-warning-message" style="display: none;"></div> </div> <div id='dd-helper' style="display: none;"></div> <noscript> <div class="overlay overlay-background noscript-overlay"> <div> <h3 class="title">Javascript Required for Galaxy</h3> <div> The Galaxy analysis interface requires a browser with Javascript enabled.<br> Please enable Javascript and refresh this page. </div> </div> </div> </noscript> <script src="/galaxy/static/scripts/bundled/libs.bundled.js?v=1489572328" type="text/javascript"></script> <script src="/galaxy/static/scripts/bundled/login.bundled.js?v=1489572328" type="text/javascript"></script> <script type="text/javascript"> app( {"redirect": "/galaxy/datasets/xxxxxxxxxxxxxxxx/display", "show_welcome_with_login": false, "user": {"quota_percent": null, "id": null, "total_disk_usage": 0.0, "nice_total_disk_usage": "0 bytes"}, "openid_providers": [], "root": "/galaxy/", "config": {"communication_server_host": "http://localhost", "ftp_upload_site": null, "mailing_lists": "https://wiki.galaxyproject.org/MailingLists", "nginx_upload_path": "/galaxy/api/tools", "terms_url": null, "enable_unique_workflow_defaults": false, "wiki_url": " https://wiki.galaxyproject.org/", "version_major": "16.07", "support_url": " https://wiki.galaxyproject.org/Support", "persistent_communication_rooms": [], "remote_user_logout_href": null, "message_box_content": null, "logo_src": "/galaxy/static/images/galaxyIcon_noText.png", "biostar_url_redirect": "http://{GALAXY_URL}/galaxy/biostar/biostar_redirect", "message_box_visible": false, "ftp_upload_dir": "{ftp_upload_dir}", "logo_url": "/galaxy/", "brand": "{BRAND}", "search_url": " http://galaxyproject.org/search/usegalaxy/", "screencasts_url": null, "ga_code": null, "require_login": true, "communication_server_port": 7070, "lims_doc_url": "https://usegalaxy.org/u/rkchak/p/sts", "inactivity_box_content": "Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address.", "citation_url": "https://wiki.galaxyproject.org/CitingGalaxy", "allow_user_creation": false, "is_admin_user": false, "allow_user_dataset_purge": true, "server_startttime": 1489572328, "biostar_url": null, "datatypes_disable_auto": false, "use_remote_user": null, "message_box_class": "info"}, "welcome_url": "/galaxy/root/welcome"}, {} ); </script> </body> </html> *Thanks and Regards,* *Ashok Varadharajan*

1 0

bowtie2 indexes & errors
by Nikolaos Tur 21 Mar '17

21 Mar '17

Hi, I observe next error: [2017-03-21 10:30:56] Beginning TopHat run (v2.1.0) ----------------------------------------------- [2017-03-21 10:30:56] Checking for Bowtie Bowtie version: 2.2.5.0 [2017-03-21 10:30:56] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (/home/galaxy/tool-data/GRCm38_84/bowtie2_index/GRCm38_84/GRCm38_84.*.bt2) And this error is clear: no index files with *.bt2. But we have for GRCm38_84: ../GRCm38_84/GRCm38_84.3.bt2l ../GRCm38_84/GRCm38_84.rev.1.bt2l ../GRCm38_84/GRCm38_84.1.bt2l ../GRCm38_84/GRCm38_84.rev.2.bt2l ../GRCm38_84/GRCm38_84.2.bt2l ../GRCm38_84/GRCm38_84.4.bt2l ../GRCm38_84/GRCm38_84.fa as I understand from the manual for bowtie2 "l" at the end of files means that indexes were created for large file. If it is correct way then why Galaxy tools do not understand this extension and how it should be solve? Okay I have simply created symbolic links to them with *.bt2 extensions (I don't know if *.tb2 and *.tb2l have the same format) and run job again: [2017-03-21 11:40:41] Beginning TopHat run (v2.1.0) ----------------------------------------------- [2017-03-21 11:40:41] Checking for Bowtie Bowtie version: 2.2.5.0 [2017-03-21 11:40:41] Checking for Bowtie index files (genome).. [2017-03-21 11:40:41] Checking for reference FASTA file [2017-03-21 11:40:41] Generating SAM header for /home/galaxy/tool-data/GRCm38_84/bowtie2_index/GRCm38_84/GRCm38_84 [2017-03-21 11:40:50] Preparing reads left reads: min. length=101, max. length=101, 37099122 kept reads (11326 discarded) right reads: min. length=101, max. length=101, 36957824 kept reads (152624 discarded) [2017-03-21 12:11:25] Mapping left_kept_reads to genome GRCm38_84 with Bowtie2 [FAILED] Error running bowtie: Error reading _plen[] array: 895748346, 4294967292 Error: Encountered internal Bowtie 2 exception (#1) Command: /home/galaxy/tools/dependencies/bowtie2/2.2.5/iuc/package_bowtie_2_2_5/30bd7eaeddbf/bin/bowtie2-align-s --wrapper basic-0 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 8 --sam-no-hd -x /home/galaxy/tooldata/GRCm38_84/bowtie2_index/GRCm38_84/GRCm38_84 - (ERR): bowtie2-align exited with value 1 If this is not an extension problem then what is an origin of this error and how to solve it? Thanx, Nikolaos

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galaxy-dev March 2017