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ProFTPD Config Issues
by Panzer, Adam 05 Sep '13

05 Sep '13

Hello Devs, I've been trying for a while now to get ProFTPD working for our local instance. I have: 1) Modified pg_hba.conf 2) Set up the ProFTPD config files 3) Disabled PBKDF2 password encryption by adding use_pbkdf2 = false to universe_wsgi.ini I've read through the posts from others with this issue and made sure to avoid some of the common pitfalls like forgetting to install/enable mod_sql.c, mod_sql_postgres.c, and LoadModule mod_sql_passwd.c or having an incorrect/<999 uid/gid in proftpd.conf. Even so, when I attempt to access the server through FileZilla, it continues to kick back login errors for all users: Status: Resolving address of localhost Status: Connecting to 127.0.0.1:21... Status: Connection established, waiting for welcome message... Response: 220 ProFTPD 1.3.4a Server (Jay2) [::ffff:127.0.0.1] Command: USER panzer_a(a)kids.wustl.edu Response: 331 Password required for panzer_a(a)kids.wustl.edu Command: PASS *********** Response: 530 Login incorrect. Error: Critical error Error: Could not connect to server I have included the contents of the relevant config files and logs below. The proftpd log says that the user name is wrong, but the sqllog seems to indicate a successful hit on the user but a failed password authentication (again, despite disabling PBKDF2). I would be most grateful if someone could tell me what I'm doing wrong. Thanks, Adam - PACKAGE VERSIONS - PostgreSQL 9.2 Nginx 1.1.19 ProFTPD 1.3.4a - PG_HBA.CONF - local all all trust host all all 127.0.0.1/32 trust host all all ::1/128 trust host all all 0.0.0.0/0 md5 - PROFTPD.CONF - Include /etc/proftpd/modules.conf UseIPv6 on IdentLookups off ServerType standalone DeferWelcome off MultilineRFC2228 on DefaultServer on ShowSymlinks on TimeoutNoTransfer 600 TimeoutStalled 600 TimeoutIdle 1200 DisplayLogin welcome.msg DisplayChdir .message true ListOptions "-l" DenyFilter \*.*/ Port 21 PassivePorts 30000 40000 MaxInstances 30 User galaxy Group galaxy Umask 077 AllowOverwrite on AuthOrder mod_sql.c SQLDefaultGID 1001 SQLDefaultUID 1001 TransferLog /var/log/proftpd/xferlog SystemLog /var/log/proftpd/proftpd.log <IfModule mod_quotatab.c> QuotaEngine off </IfModule> <IfModule mod_ratio.c> Ratios off </IfModule> <IfModule mod_delay.c> DelayEngine on </IfModule> <IfModule mod_ctrls.c> ControlsEngine off ControlsMaxClients 2 ControlsLog /var/log/proftpd/controls.log ControlsInterval 5 ControlsSocket /var/run/proftpd/proftpd.sock </IfModule> <IfModule mod_ctrls_admin.c> AdminControlsEngine off </IfModule> Include /etc/proftpd/conf.d/ - GALAXY.CONF (galaxy specific conf.d ProFTPD config file) - ServerName "Jay2" DefaultRoot ~ CreateHome on dirmode 700 AllowOverwrite on AllowStoreRestart on <Limit SITE_CHMOD> DenyAll </Limit> <Limit RETR> DenyAll </Limit> AuthPAM off SQLPasswordEngine on SQLPasswordEncoding hex SQLEngine on SQLBackend postgres SQLConnectInfo galaxy@localhost:5432 galaxy galaxy SQLAuthTypes SHA1 SQLAuthenticate users SQLDefaultHomedir /var/lib/proftpd/empty SQLUserInfo custom:/LookupGalaxyUser SQLNamedQuery LookupGalaxyUser SELECT "email,password,'1001','1001','/home/galaxy/galaxy-supp/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" SQLLogFile /var/log/proftpd/sqlLog.txt - PROFTPD.LOG - Sep 04 19:03:51 PCF10-WKS1572 proftpd[4846] PCF10-WKS1572 (localhost[127.0.0.1]): FTP session closed. Sep 04 19:14:57 PCF10-WKS1572 proftpd[5034] PCF10-WKS1572 (localhost[127.0.0.1]): FTP session opened. Sep 04 19:14:57 PCF10-WKS1572 proftpd[5034] PCF10-WKS1572 (localhost[127.0.0.1]): USER panzer_a(a)kids.wustl.edu (Login failed): No such user found. - SQLLOG.TXT - Sep 04 19:14:57 mod_sql/4.3[5034]: defaulting to 'postgres' backend Sep 04 19:14:57 mod_sql/4.3[5034]: backend module 'mod_sql_postgres/4.0.4' Sep 04 19:14:57 mod_sql/4.3[5034]: backend api 'mod_sql_api_v1' Sep 04 19:14:57 mod_sql/4.3[5034]: >>> sql_sess_init Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_defineconnection Sep 04 19:14:57 mod_sql/4.3[5034]: name: 'default' Sep 04 19:14:57 mod_sql/4.3[5034]: user: 'galaxy' Sep 04 19:14:57 mod_sql/4.3[5034]: host: 'localhost' Sep 04 19:14:57 mod_sql/4.3[5034]: db: 'galaxy' Sep 04 19:14:57 mod_sql/4.3[5034]: port: '5432' Sep 04 19:14:57 mod_sql/4.3[5034]: ttl: '0' Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_defineconnection Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' successfully established Sep 04 19:14:57 mod_sql/4.3[5034]: mod_sql engine : on Sep 04 19:14:57 mod_sql/4.3[5034]: negative_cache : off Sep 04 19:14:57 mod_sql/4.3[5034]: authenticate : users Sep 04 19:14:57 mod_sql/4.3[5034]: usertable : users Sep 04 19:14:57 mod_sql/4.3[5034]: userid field : userid Sep 04 19:14:57 mod_sql/4.3[5034]: password field : passwd Sep 04 19:14:57 mod_sql/4.3[5034]: UID field : uid Sep 04 19:14:57 mod_sql/4.3[5034]: GID field : gid Sep 04 19:14:57 mod_sql/4.3[5034]: homedir field : homedir Sep 04 19:14:57 mod_sql/4.3[5034]: homedir(default) : '/var/lib/proftpd/empty' Sep 04 19:14:57 mod_sql/4.3[5034]: shell field : shell Sep 04 19:14:57 mod_sql/4.3[5034]: SQLMinUserUID : 999 Sep 04 19:14:57 mod_sql/4.3[5034]: SQLMinUserGID : 999 Sep 04 19:14:57 mod_sql/4.3[5034]: <<< sql_sess_init Sep 04 19:14:57 mod_sql/4.3[5034]: >>> sql_pre_pass Sep 04 19:14:57 mod_sql/4.3[5034]: <<< sql_pre_pass Sep 04 19:14:57 mod_sql/4.3[5034]: >>> cmd_getpwnam Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_escapestring Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: Postgres server version: 9.2.4 Sep 04 19:14:57 mod_sql/4.3[5034]: Postgres connection character set now 'UTF8' (from 'UTF-8') Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' opened Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 2 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 1 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_escapestring Sep 04 19:14:57 mod_sql/4.3[5034]: cache miss for user 'panzer_a(a)kids.wustl.edu' Sep 04 19:14:57 mod_sql/4.3[5034]: >>> sql_lookup Sep 04 19:14:57 mod_sql/4.3[5034]: >>> process_named_query 'LookupGalaxyUser' Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_escapestring Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 2 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 1 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_escapestring Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_escapestring Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 2 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 1 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_escapestring Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_select Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 2 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: query "SELECT email,password,'1001','1001','/home/galaxy/galaxy-supp/ftp/panzer_a(a)kids.wustl.edu','/bin/bash' FROM galaxy_user WHERE email='panzer_a(a)kids.wustl.edu'" Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 1 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_select Sep 04 19:14:57 mod_sql/4.3[5034]: <<< process_named_query 'LookupGalaxyUser' Sep 04 19:14:57 mod_sql/4.3[5034]: <<< sql_lookup Sep 04 19:14:57 mod_sql/4.3[5034]: cache miss for user 'panzer_a(a)kids.wustl.edu' Sep 04 19:14:57 mod_sql/4.3[5034]: user 'panzer_a(a)kids.wustl.edu' cached Sep 04 19:14:57 mod_sql/4.3[5034]: + pwd.pw_name : panzer_a(a)kids.wustl.edu Sep 04 19:14:57 mod_sql/4.3[5034]: + pwd.pw_uid : 1001 Sep 04 19:14:57 mod_sql/4.3[5034]: + pwd.pw_gid : 1001 Sep 04 19:14:57 mod_sql/4.3[5034]: + pwd.pw_dir : /home/galaxy/galaxy-supp/ftp/panzer_a(a)kids.wustl.edu Sep 04 19:14:57 mod_sql/4.3[5034]: + pwd.pw_shell : /bin/bash Sep 04 19:14:57 mod_sql/4.3[5034]: <<< cmd_getpwnam Sep 04 19:14:57 mod_sql/4.3[5034]: >>> cmd_auth Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_escapestring Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 2 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_open Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 1 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_escapestring Sep 04 19:14:57 mod_sql/4.3[5034]: cache hit for user 'panzer_a(a)kids.wustl.edu' Sep 04 19:14:57 mod_sql/4.3[5034]: >>> cmd_check Sep 04 19:14:57 mod_sql/4.3[5034]: checking password using SQLAuthType 'sha1' Sep 04 19:14:57 mod_sql/4.3[5034]: 'sha1' SQLAuthType handler reports failure Sep 04 19:14:57 mod_sql/4.3[5034]: <<< cmd_check Sep 04 19:14:57 mod_sql/4.3[5034]: <<< cmd_auth Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_exit Sep 04 19:14:57 mod_sql/4.3[5034]: entering postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' closed Sep 04 19:14:57 mod_sql/4.3[5034]: connection 'default' count is now 0 Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_close Sep 04 19:14:57 mod_sql/4.3[5034]: exiting postgres cmd_exit The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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tool-shed migration - dist version still shown in UI
by Shantanu Pavgi (Campus) 05 Sep '13

05 Sep '13

I have migrated few tools from dist to tool-shed and I am seeing two version select options in the UI. Both option contain same version number though. One of them is linking to dist path (underneath tools directory) and other one is using tool-shed path. The dist path isn't in place after the migration completed so if one selects that version option, then job fails. The tool-shed versioned path is working fine. The migrated tool xml file and integrated tool xml file both contain tool-shed related entries. Appreciate any help on how to fix this issue. Any pointers? -- Thanks, Shantanu [cid:2E575F19-219F-450F-BB27-6D7E63292D3E@bham.rr.com]

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iRODS integration
by Zeeshan Ali Shah 05 Sep '13

05 Sep '13

Hi All, Is there any update on iRods integration in galaxy ? One major concern presented in deployment of Galaxy is that all of the researcher data is access by a user id (linux) running galaxy server. This is typical webserver problem. May be it is some how resolved by iRods or any other better Authn based FS. any suggestion ? -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah

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Trackster: alignment is not showing up as 'squish'
by Joachim Jacob | VIB | 05 Sep '13

05 Sep '13

Hi all, I have a problem that the mappings of an experiment suddenly don't show up anymore in Trackster, only when I choose 'squish' as visualisation format. 'Coverage' and 'dense' provide the expected output. So 'squish' shows nothing. But 'Pack' shows only the names, without the bars. Note: 'squish' and 'pack' used to work. Currently I am on 2013_08_12. Other mappings (from other experiments) show up as expected. The 2 cases side by side in this screenshot (thanks to the scratchbook functionality!): https://dl.dropboxusercontent.com/u/18352887/Selection_151.png Thanks for any help, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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For constructing workflow of workflows
by patra 05 Sep '13

05 Sep '13

Hi, This is Deblina. I am working as a PhD student in Martin Luther University Wittenberg, Halle, Germany. For a project I want to use Galaxy. I need to construct a master workflow with sub-workflows connected to each other. Is it possible to construct "workflows of workflows" in galaxy? Best Regards, Deblina.

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Mercurial updates not working
by Alistair Chilcott 04 Sep '13

04 Sep '13

Hello all, Mercurial has recently started throwing errors: galaxy@hitmsbhpc1:~/galaxy-dist> hg incoming abort: error: _ssl.c:517: error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol It has previously worked with issues has anyone seen this before? I don't think anything has changed that would have caused this problem but googling error has proved to be unhelpful so far. Regards, Alistair

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Typo in Wiki Page - Purge History and Datasets
by Adam Brenner 04 Sep '13

04 Sep '13

http://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20… > There are 5 scripts included in the Galaxy distribution that > can be used to clean up unwanted histories, libraries and > datasets. There are located in the <<<nwwl(GALAXY_ROOT)>>>/scripts/cleanup_datasets > directory and are named: Should be changed to 6 scripts Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

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about Galaxy
by Jennifer Jackson 04 Sep '13

04 Sep '13

Hello, To use Velvet, a local, cloud, or slipstream Galaxy is needed. Then the tool can be installed from the Tool Shed and used. The screencasts "Introduction to Galaxy ToolShed 1/2/3" walk through the general process when using CloudMan Galaxy: http://vimeo.com/user20484153 http://wiki.galaxyproject.org/Cloud http://wiki.galaxyproject.org/BigPicture/Choices If you need help with set up, or just have more questions about these options, the list is: "galaxy-dev(a)bx.psu.edu" http://wiki.galaxyproject.org/MailingLists Best, Jen Galaxy team On 9/4/13 5:31 AM, Jingjing Peng wrote: > Hi, > Nowadays I am using Galaxy to analyze my data. It is really very good. > But there is sth I cannot work it out by this program. My sequences > were sequenced by Illumina Miseq 2*250bp,paired end method. I want to > assembly this large transcriptom sequences. I didn't find velvet in > this website:https://main.g2.bx.psu.edu/ . > So how can I find it and make this work. I am sorry to trouble you. > Thanks a lot. > > Best wishes, > > Jingjing Peng > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Accessing parameter defined within conditional from option filter
by Peter Briggs 04 Sep '13

04 Sep '13

Hello Galaxy folks I'm building a tool to run the Trimmomatic program, and I've encountered an issue with filtering options from an external .loc file based on the value of a parameter which is defined within a conditional block. The parameter definition looks like this: ... <conditional name="paired_end"> <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" /> <when value="no"> ... Subsequently I try to access the value of "is_paired_end" within a filter tag (to select a subset of items from a .loc file), using "ref_attribute" (based on the assumption that I'm trying to access "paired_end.is_paired_end"): ... <options from_file="adapters.loc"> <filter type="param_value" column="1" ref="paired_end" ref_attribute="is_paired_end" /> ... However this doesn't work, in that no options are returned by the filter. A debug statement in the relevant code for the ParamValueFilter (in dynamic_options.py) tells me that there's no "is_paired_end" attribute. The only other tool I could find which uses "ref_attribute" is bfast_wrapper.xml, but this is accessing the "extension" attribute of a parameter not within a conditional (i.e. not the same as my example). Should it be possible to do what I'm trying? Or is there a different way to do it? Thanks for any help or suggestions, Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Updating Galaxy Instance
by Richard Kuo 03 Sep '13

03 Sep '13

I can't seem to find any information on the Galaxy wiki website about the procedure for updating a local Galaxy instance to the newest release. Is there a tutorial for this somewhere? Thank you, Richard

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