July 2013 - galaxy-dev - lists.galaxyproject.org

Running additional services
by Rob Leclerc 22 Jul '13

22 Jul '13

We're running cloudman and I would like to run a couple of additional services alongside galaxy. Is there a elegant way/place to add/run these services to existing galaxy code/scripts? Cheers, Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-5469 Personal Email: rob.leclerc(a)aya.yale.edu

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Problem with tophat in local instance
by Rainy Luo 22 Jul '13

22 Jul '13

Hi,all, I am a beginner of Galaxy.Because I need to analyze large-scale deep-seq data and the pubic Galaxy serve did not work out,I installed linux(the first time to use linux) and set up the local galaxy instance in my computer. It seemed everything worked fine until I tried to use Tophat to align the reads to the reference genome.The problem is although I have already downloaded the Refgenome from UCSC,when I use the Tophat,"select a reference genome"option is empty. is there anybody having similar problem?How to deal with it? Thanks! Rainy

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Adding files to a data library - genome option
by Lionel Guy 22 Jul '13

22 Jul '13

Hi Galaxy-devs, When adding files to a data library (as admin), I have to choose the genome corresponding to my dataset, but the drop-down list is not sorted, making it a tad annoying to scroll. In addition, by default, the homIni20 genome is selected, which seems a bit anthropocentric ;) I would suggest that the genome drop-down list has the same behavior as the one in the Upload File tool (i.e. sorted alphabetically, with "unspecified" as the default value). Not sure this is a bug or even worth a Trello card, so I post it here. I'd be happy to fill in a Trello card if requested. Cheers, Lionel

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ToolShed preview lacking controls
by Peter Cock 22 Jul '13

22 Jul '13

HI all, I just had a query about some 'missing' functionality in one of my tools, which is handled by a parameter which doesn't get shown on the preview shown in the Tool Shed - perhaps because it is inside a conditional? <conditional name="output_choice_cond"> <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?"> <option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two files</option> <option value="pos">Just positive matches (ID on list), as a single file</option> <option value="neg">Just negative matches (ID not on list), as a single file</option> </param>  <when value="both" /> <when value="pos" /> <when value="neg" /> </conditional> Ideally the ToolShed preview would show the dropdown combo box allowing you to pick both files, positive only, or negative only: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id Is this a known limitation? Is there a Trello card I should follow? Thanks, Peter

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unable to display text output
by mark.rose＠syngenta.com 22 Jul '13

22 Jul '13

Hi All I'm trying to format one of the three outputs of my galaxy tool as plain text. Thus far no matter how I specify my output format in the tool xml file I have the same problem. When I click the eye icon it opens a save dialog rather that displaying the text output in the central frame. The preview shows the text output and if I follow through and save the output and open with wordpad it is fine. Also if I edit the attributes of the output and change it to "txt" (which is one of the formats I had tried specifying in the xml) it will render in the central frame but I would rather not have to do that. Both of my other outputs (a vcf and a tab-delimited file) are rendered in the central frame properly. How do I to fix this? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Manual modifications to integrated_tool_panel.xml?
by Dan Sullivan 22 Jul '13

22 Jul '13

Hi, Galaxy Developers, I have what I believe to be a basic question/problem with respect to making modifications to the integrated_tool_panel.xml (and or tool_conf.xml). Our Galaxy deployment does have some custom additions made to these files (I did not make these modifications so I am not 100% certain at this point whether or not the modifications to integrated_tool_panel.xml were manual or propagated from elsewhere) , and everything seems to work alright, although I do have a problem that I am having somewhat of a difficult time resolving. Before ask my question, I wanted to confirm my understanding of the wiki page http://wiki.galaxyproject.org/GalaxyToolPanel. I was hoping that somebody could validate the following statements; 1) The only thing that a human being should really ever change in the file "integrated_tool_panel.xml" is the ordering of the groupings (I believe I read on the developer mailing list that it was acceptable to delete sections from here as well, although I am not attempting to validate this at this time). 2) That for all intensive purposes, the integrated_tool_panel.xml should be generated automatically from the files specified in the "tool_config_file" configuration directive in universe_wsgi.ini. 3) That it is perfectly to acceptable to make manual modifications to XML files supplied in the configuration directive "tool_config_file" in the universe_wsgi.ini, or add any number additional XML files to this list (presumably I wouldn't want to make too many manual changes to the shed_tool_conf.xml file, I'm referring to the other XML files, not this one). The reason I am asking this question is a fairly simple one; every now and then, it appears that new tools are released when new versions of Galaxy are released (i.e. a slightly different default toolset is offered, and thus tool panel and or tool configuration files are generated when the new version of Galaxy is started, at least if I do a fresh install). It appears to me based on some very basic testing that once a manual modification to the tool_conf.xml is made, that the next time a pull for an update is run and Galaxy is restarted, that these files remain as-is; basically, what appears to be happening is that we are running a new version of Galaxy with what seems to be an out-of-date integrated_tool_panel.xml, at least in terms of the tools that are configured as part of the default install; this, in a nutshell, is the fundamental problem I am currently dealing with. Here is what I'm thinking is the "correct" way to solve my problem; 1) Since we are manually modifying the tools_conf.xml, It seems to me that we are kind of shooting ourselves in the foot in terms of our ability to delete this file and have Galaxy update it when we do an upgrade . Based on what I know I feel that we should do is take all of our custom tools modifications and put them in a separate file called uofc_custom_tools.xml, and then add that to "tool_config_file" to abstract away our custom tool configurations from the default tool_conf.xml. 2) When we upgrade galaxy, delete the tools_conf.xml, and when galaxy starts, let it replace this file with the default from the current changeset. 3) As long as we didn't need to do any manually reordering of elements in the integrated_tool_panel.xml, just delete the integrated_tool_panel.xml, and allow it to be manually re-generated from tool_conf.xml and uofc_custom_tools.xml. Does this solution sound reasonable? I would be very grateful on any insight anybody could provide in the best way to address this problem. I wish you a wonderful day. Dan Sullivan

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Re: [galaxy-dev] ProFTPD integration with Galaxy
by TerryYeh＠NARL 22 Jul '13

22 Jul '13

Dear All, I am having a similar problem too. I followed the config setting provide by Mr. Perez and modified some possible error. I still cannot login my ftp server. Following is my proftpd.conf. Please help me to figure out the problem. Thanks a lot!! # This is a basic ProFTPD configuration file (rename it to # 'proftpd.conf' for actual use. It establishes a single server # and a single anonymous login. It assumes that you have a user/group # "nobody" and "ftp" for normal operation and anon. ServerName "ProFTPD Default Installation" ServerType standalone DefaultServer on # Port 21 is the standard FTP port Port 2121 # Don't use IPv6 support by default. UseIPv6 off # Umask 022 is a good standard umask to prevent new dirs and files # from being group and world writable. Umask 022 # To prevent DoS attacks, set the maximum number of child processes # to 30. If you need to allow more than 30 concurrent connections # at once, simply increase this value. Note that this ONLY works # in standalone mode, in inetd mode you should use an inetd server # that allows you to limit maximum number of processes per service # (such as xinetd). MaxInstances 30 # Set the user and group under which the server will run. User username Group groupname PassivePorts 40000 40999 # To cause every FTP user to be "jailed" (chrooted) into their home # directory, uncomment this line. #DefaultRoot ~ CreateHome on dirmode 700 # Normally, we want files to be overwriteable. AllowOverwrite on AllowStoreRestart on # Bar use of SITE CHMOD by default <Limit SITE_CHMOD> DenyAll </Limit> <Limit RETR> DenyAll </Limit> <IfModule mod_dso.c> LoadModule mod_sql.c LoadModule mod_sql_passwd.c LoadModule mod_sql_postgres.c </IfModule> SQLLogFile /pkg/biology/galaxy/proftpd/log/proftpd-sql-local ## ServerLog /pkg/biology/galaxy/proftpd/var/proftpd-server.log SystemLog /pkg/biology/galaxy/proftpd/var/proftpd-system.log #AuthPAMConfig ftp #AuthOrder mod_auth_pam.c* mod_auth_unix.c # Do not authenticate against real (system) users AuthPAM off #AuthOrder mod_sql.c # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1 SQLPasswordEngine on SQLPasswordEncoding hex # Set up mod_sql to authenticate against the Galaxy database SQLEngine on SQLBackend postgres SQLConnectInfo galaxy@localhost username password SQLAuthTypes SHA1 SHA256 pbkdf2 SQLPasswordPBKDF2 SHA256 10000 24 SQLAuthenticate users # An empty directory in case chroot fails #SQLDefaultHomedir /var/opt/local/proftpd # Define a custom query for lookup that returns a passwd-like entry. UID and GID should match your Galaxy user. SQLUserInfo custom:/LookupGalaxyUser SQLPasswordUserSalt sql:/GetUserSalt #SQLNamedQuery LookupGalaxyUser SELECT "email,password,'12345','1234','/home/username/galaxyftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLNamedQuery LookupGalaxyUser SELECT "email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 32) ELSE password END) AS password,'12345','1234','/home/username/galaxyftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLNamedQuery GetUserSalt SELECT "(CASE WHEN SUBSTRING (password from 1 for 6) = 'PBKDF2' THEN SUBSTRING (password from 21 for 16) END) AS salt FROM galaxy_user WHERE email='%U'" I still get the message of authentication failed. 2013-07-22 11:07:29,590 mod_sql/4.3[8124]: checking password using SQLAuthType 'sha1' 2013-07-22 11:07:29,590 mod_sql/4.3[8124]: 'sha1' SQLAuthType handler reports failure 2013-07-22 11:07:29,590 mod_sql/4.3[8124]: checking password using SQLAuthType 'sha256' 2013-07-22 11:07:29,590 mod_sql/4.3[8124]: 'sha256' SQLAuthType handler reports failure 2013-07-22 11:07:29,590 mod_sql/4.3[8124]: checking password using SQLAuthType 'pbkdf2' 2013-07-22 11:07:29,619 mod_sql/4.3[8124]: 'pbkdf2' SQLAuthType handler reports failure Any suggestion on my configuration file, Thanks.

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Invitation to connect on LinkedIn
by sachit adhikari 21 Jul '13

21 Jul '13

LinkedIn ------------ galaxy-dev(a)bx.psu.ed, I'd like to add you to my professional network on LinkedIn. - sachit sachit adhikari Software Engineer at ZurelSoft Nepal Nepal Confirm that you know sachit adhikari: https://www.linkedin.com/e/1kvf56-hjf9os56-3g/isd/15160415460/FH4R02On/?hs=… -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/1kvf56-hjf9os56-3g/qaQIbd-APagZF22GBAQuFmcZcI_00a… (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Rename output while initiating the task in galaxy
by Sachit Adhikari 21 Jul '13

21 Jul '13

Hi group, The galaxy stores the output of the job on files/043/dataset_*ID*.dat. I have two questions here.: 1) Can I find the ID of my output from the Galaxy history? I tried Edit Attributes, Annotations, tags but couldn't find it. 2) Can I rename my output while initiating the task? If I can how can I do this and what are the consequences. Thank you. Regards, Sachit

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job status error in the history panel
by Philipe Moncuquet 21 Jul '13

21 Jul '13

Hi all, While in Oslo I heard about the bug that make your job always appeared in queue mod unless you refresh your history. Now that we have updated our own instance I see that bug and was wondering want we can do about it. I haven't seen anything on the mailing list but if I miss the thread please point it to me. Regards, Philippe

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