[galaxy-dev] Invitation to connect on LinkedIn
LinkedIn galaxy-...@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=falsetok=0gQT6_MazFyRQ1 -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/1kvf56-hjf9os56-3g/qaQIbd-APagZF22GBAQuFmcZcI_00a44mJ/goo/galaxy-dev%40bx%2Epsu%2Eedu/20061/I5047310806_1/?hs=falsetok=2tRUJSiarFyRQ1 (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ProFTPD integration with Galaxy
Hi, 1/ Do you know who is your (FTP) galaxy user ? The proftpd daemon should run whith this user (be carefull to permissions). 2/ Did you try a simpler way to authenticate to your postgresql server ? I mean, you choose to add some parameter as SQLPasswordPBKDF2 or SQLPasswordUserSalt. You should know what kind of algorithm is used to encrypt password on your postgres server and then use it... Follow this tutorial : http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP If it works, then add 'salt' method if you wish, or other algorithm/method to encrypt password... Regards 2013/7/22 TerryYeh@NARL terry...@nchc.narl.org.tw 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 Port2121 ** ** # 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). MaxInstances30 ** ** # Set the user and group under which the server will run. Userusername Group groupname ** ** ** ** PassivePorts4 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 SQLAuthTypesSHA1 SHA256 pbkdf2 SQLPasswordPBKDF2 SHA256 1 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' SQLNamedQueryLookupGalaxyUser 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' SQLNamedQueryGetUserSalt SELECT (CASE WHEN SUBSTRING (password from 1 for 6) =
[galaxy-dev] Manual modifications to integrated_tool_panel.xml?
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ProFTPD integration with Galaxy
Sorry, I didn't see the recent changes... 2013/7/22 Rémy Dernat remy...@gmail.com Hi, 1/ Do you know who is your (FTP) galaxy user ? The proftpd daemon should run whith this user (be carefull to permissions). 2/ Did you try a simpler way to authenticate to your postgresql server ? I mean, you choose to add some parameter as SQLPasswordPBKDF2 or SQLPasswordUserSalt. You should know what kind of algorithm is used to encrypt password on your postgres server and then use it... Follow this tutorial : http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP If it works, then add 'salt' method if you wish, or other algorithm/method to encrypt password... Regards 2013/7/22 TerryYeh@NARL terry...@nchc.narl.org.tw 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 Port2121 ** ** # 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). MaxInstances30 ** ** # Set the user and group under which the server will run. Userusername Group groupname ** ** ** ** PassivePorts4 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 SQLAuthTypesSHA1 SHA256 pbkdf2 SQLPasswordPBKDF2 SHA256 1 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' SQLNamedQueryLookupGalaxyUser 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
Re: [galaxy-dev] ProFTPD integration with Galaxy
I noticed the errors in the SUBSTRING length too and I modified my configuration file accordingly but still not able to authenticate :( F. Il 22/07/13 05.40, TerryYeh@NARL ha scritto: 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). MaxInstances30 # Set the user and group under which the server will run. User username Group groupname PassivePorts 4 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 1 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' SQLNamedQueryGetUserSalt 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. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Federico Zambelli, Ph.D. Bioinformatics, Evolution and Comparative Genomics Lab Dept. of Biosciences University of Milano - Italy What can be asserted without proof can be dismissed without proof. ___ Please keep all replies on the list by using reply all in your mail client.
[galaxy-dev] ToolShed preview lacking controls
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=bothBoth positive matches (ID on list) and negative matches (ID not on list), as two files/option option value=posJust positive matches (ID on list), as a single file/option option value=negJust negative matches (ID not on list), as a single file/option /param !-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -- 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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] unable to display text output
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. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Manual modifications to integrated_tool_panel.xml?
Hi Dan, 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? Yes :)! Having local modifications in a separate file makes totally sense! Step 2. is not necessary, imho, you can also merge both files tools_conf.xml and tools_conf.xml.sample if you like. 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. You too! Bjoern Dan Sullivan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ToolShed preview lacking controls
Hi Peter, This is a known issue - there is a Trello card for it here: https://trello.com/c/3sAsMYFc/588-toolshed-fix-display-of-conditional-objects-in-display-tool-action Thanks, Greg Von Kuster On Jul 22, 2013, at 9:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote: 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=bothBoth positive matches (ID on list) and negative matches (ID not on list), as two files/option option value=posJust positive matches (ID on list), as a single file/option option value=negJust negative matches (ID not on list), as a single file/option /param !-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -- 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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ToolShed preview lacking controls
On Mon, Jul 22, 2013 at 3:03 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, This is a known issue - there is a Trello card for it here: https://trello.com/c/3sAsMYFc/588-toolshed-fix-display-of-conditional-objects-in-display-tool-action Thanks, Greg Von Kuster Thanks Greg - I've subscribed voted for that issue :) Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome
On Mon, Jul 22, 2013 at 10:40 AM, Moritz Juchler juch...@stud.uni-heidelberg.de wrote: Hey, now I am having a new problem: Convert SAM to BAM Tool execution generated the following error message: [samopen] SAM header is present: 93 sequences. Parse error at line 106: sequence and quality are inconsistent /bin/sh: line 1: 27934 Aborted samtools view -bS /home/trr/galaxy-dist/database/files/000/dataset_17.dat /tmp/tmp-sam_to_bam_converter-ut5Tag/unsorted.bam That's bad. The tool produced the following additional output: [bam_header_read] EOF marker is absent. The input is probably truncated. (should I make a new post out of this?) Which version of samtools? There is a bug in the currently release where that warning is a false alarm: https://github.com/samtools/samtools/issues/18 Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] workflow: default parameters
Not currently possible, but it shouldn't be too difficult to make work. Please file a Trello card. On Tue, Jul 9, 2013 at 11:36 AM, Keilwagen, Jens jens.keilwa...@jki.bund.de wrote: when building workflows we can choose for each parameter whether to 'set at runtime' or to 'set in advance' (when creating or editing the workflow). We are looking for a possiblity to set a default value that is used (only) for the workflow, i.e., we like to specify a value that might be used by most users, but might be altered by expert users. This value might be different from the default value of the corresponding tool. So far, we did not find any possiblity. -- James Taylor, Assistant Professor, Biology/CS, Emory University ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Adding files to a data library - genome option
That's both a bug (should default to 'unspecified') and a usability issue (sorting the genomes). I've added a card: https://trello.com/c/Hr1JdeGq/1007-ui-bug-genome-selection-when-adding-library-data-files On Thu, Jul 11, 2013 at 11:06 AM, Lionel Guy guy.lio...@gmail.com wrote: 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 __**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/**search/mailinglists/http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Problem with tophat in local instance
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 genomeoption is empty. is there anybody having similar problem?How to deal with it? Thanks! Rainy ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] unable to display text output
Hi Mark Quick answer: It could be an issue with your browser. Have you tried looking at your date with a different web browser and/or on a different machine? Long answer: Could you please clarify, as I can't really follow your description of the problemyou say: it is working if you change the data format manually to 'txt', but it is not working if you specify it as 'txt' in the tool xml? And when you specify it as 'txt' in the tool xml do you get format: txt, in the history display? Regards, Hans-Rudolf On Jul 22, 2013, at 3:27 PM, mark.r...@syngenta.commailto:mark.r...@syngenta.com wrote: 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.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome
Hey, with the tool file line I got it working :) Thanks a lot. Could you answer the question regarding Tool Shed: If I would use Tool Shed, could I skip all these manual steps? Is the installation of BWA with Tool Shed also this complicated or is it more simle? Best Moritz On 17 July 2013 09:51, Moritz Juchler juch...@stud.uni-heidelberg.dewrote: Hey, no thats correct I did not use Tool Shed. If I would use it, could I skip all these manual steps? Is the installation of BWA with Tool Shed also this complicated or is it more simle? How did you not follow my steps :) I wrote down everything clearly, at least thats what I was hoping. And no I didnt write this line tool file=sr_mapping/bwa_wrapper.**xml / Thats the first time, I am seeing this tutorial :( I will try this out right now Best Moritz On 17 July 2013 09:42, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Moritz I am struggling to follow what exactly you have done. As far as I can see, you did not use the toolshed (http://wiki.galaxyproject.** org/Tool%20Shed http://wiki.galaxyproject.org/Tool%20Shed) to install the BWA alinger tool, but did all manually? If so, have you added the following line: tool file=sr_mapping/bwa_wrapper.**xml / to the tool_conf.xml file, and restarted Galaxy? see also: http://wiki.galaxyproject.org/**Admin/Tools/Add%20Tool%**20Tutorialhttp://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial Hope this helps Hans-Rudolf On 07/16/2013 08:35 PM, Moritz Juchler wrote: Hello Ladies and Gentlemen, I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to choose a bioinformatic pipeline management tool to find SNP's in genomes from hcc patients. My decision was made in favor of galaxy. I have a 64-bit openSuse 11.3 server. I have installed Galaxy locally, since we have a) very large files (30GB per patient) and b) the data is protection sensitive. I kept close to http://wiki.galaxyproject.org/**Admin/Get%20Galaxyhttp://wiki.galaxyproject.org/Admin/Get%20Galaxy Now I would like to run this bpipe pipeline: http://pastebin.com/sZd5vfdL And the first step is to align my genome to a _hg19 reference genome_ which I have locally under /genedata/human_genome_GRCh37/**. trr@portalmoritz:~ ls -l /genedata/human_genome_GRCh37/ total 8486312 -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa -rw-r--r-- 1 trr root 8591 2013-07-01 16:06 hg19.fa.amb -rw-r--r-- 1 trr root 4040 2013-07-01 16:06 hg19.fa.ann -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05 hg19.fa.bwt -rw-r--r-- 1 trr root 784290318 2013-07-01 16:06 hg19.fa.pac -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31 hg19.fa.sa http://hg19.fa.sa _bwa is installed and gives me:_ trr@portalmoritz:~ bwa Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.5a-r405 Contact: Heng Li l...@sanger.ac.uk mailto:l...@sanger.ac.uk Then I tried to follow this guide: http://wiki.galaxyproject.org/**Admin/NGS%20Local%20Setuphttp://wiki.galaxyproject.org/Admin/NGS%20Local%20Setupto get the reference files and http://wiki.galaxyproject.org/**Admin/Config/Tool%**20Dependencieshttp://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies . This is my _$PATH_ trr@portalmoritz:~ echo $PATH /home/trr/bin:/usr/local/bin:/**usr/bin:/bin:/usr/bin/X11:/** usr/X11R6/bin:/usr/games:/**home/trr/bpipe-0.9.8/bin:/** home/trr/bwa-0.7.5a:/home/trr/**samtools-0.1.19 _In the universe_wsgi.ini I changed:_ tool_dependency_dir = /home/trr/galaxy-dist/tool_**dependency_dir debug = False use_interactive = True library_import_dir = /genedata/ allow_library_path_paste = True admin_users = ... This is my _tool_dependency_dir:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa ls -l total 4 drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4 lrwxrwxrwx 1 trr users6 2013-07-16 14:17 default - 0.7.4/ This is the_version folder of bwa:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4 ls -l total 8 drwxr-xr-x 2 trr users 4096 2013-07-16 14:18 bin -rw-r--r-- 1 trr users 47 2013-07-16 14:22 env.sh This is the _content of env.sh:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4 cat env.sh PATH=/home/trr/bwa-0.7.5a/:$**PATH export PATH And this is the _content of the bin folder:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4/bin ls -l total 3896 -rw-r--r-- 1 trr users 6098 2013-07-16 14:18 bamlite.c -rw-r--r-- 1 trr users 3124 2013-07-16 14:18 bamlite.h -rw-r--r-- 1 trr users 24816 2013-07-16 14:18 bamlite.o -rw-r--r-- 1 trr users 11508 2013-07-16 14:18 bntseq.c -rw-r--r-- 1 trr users 2557 2013-07-16 14:18 bntseq.h -rw-r--r-- 1 trr users 37440 2013-07-16 14:18 bntseq.o -rwxr-xr-x
[galaxy-dev] Cloudman master cannot connect to volume at start-up
* This is what has been reported by the cluster status log: * * 20:01:14 - Master starting * 20:01:16 - Trouble getting volume reference for volume vol-91cfd1cb: EC2ResponseError: 400 Bad RequestInvalidVolume.NotFoundThe volume 'vol-91cfd1cb' does not exist.9179663c-c5ec-4e90-88ff-ecf606b5e9a6 * 20:01:16 - Attempting to connect to a non-existent volume vol-91cfd1cb * 20:01:16 - Error processing filesystems in existing cluster configuration: 'NoneType' object has no attribute '__getitem__' * 20:01:16 - * Manager failed to start * Any suggestions? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Cloudman - is it possible to still use depreciated AMIs ?
I tried launching an instance specifying ami-da58aab3 as the AMI but I am unable to SSH or access Cloudman using the instance's URL. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BWA Illumina Mapping / BWA Reference Genome
Hey, now I am having a new problem: *Convert SAM to BAM *Tool execution generated the following error message: [samopen] SAM header is present: 93 sequences. Parse error at line 106: sequence and quality are inconsistent /bin/sh: line 1: 27934 Aborted samtools view -bS /home/trr/galaxy-dist/database/files/000/dataset_17.dat /tmp/tmp-sam_to_bam_converter-ut5Tag/unsorted.bam The tool produced the following additional output: [bam_header_read] EOF marker is absent. The input is probably truncated. (should I make a new post out of this?) The step I did before was: 7: *Map* with BWA for Illumina on data 5 and data 3: mapped reads ~21,000 lines, 94 comments format: sam, database: hg19 BWA Version: 0.7.5a-r405 BWA run on paired-end data That one seems to work correctly. Any help appreciated :) Best Moritz On 22 July 2013 11:20, Moritz Juchler juch...@stud.uni-heidelberg.dewrote: Hey, with the tool file line I got it working :) Thanks a lot. Could you answer the question regarding Tool Shed: If I would use Tool Shed, could I skip all these manual steps? Is the installation of BWA with Tool Shed also this complicated or is it more simle? Best Moritz On 17 July 2013 09:51, Moritz Juchler juch...@stud.uni-heidelberg.dewrote: Hey, no thats correct I did not use Tool Shed. If I would use it, could I skip all these manual steps? Is the installation of BWA with Tool Shed also this complicated or is it more simle? How did you not follow my steps :) I wrote down everything clearly, at least thats what I was hoping. And no I didnt write this line tool file=sr_mapping/bwa_wrapper.**xml / Thats the first time, I am seeing this tutorial :( I will try this out right now Best Moritz On 17 July 2013 09:42, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Moritz I am struggling to follow what exactly you have done. As far as I can see, you did not use the toolshed (http://wiki.galaxyproject.** org/Tool%20Shed http://wiki.galaxyproject.org/Tool%20Shed) to install the BWA alinger tool, but did all manually? If so, have you added the following line: tool file=sr_mapping/bwa_wrapper.**xml / to the tool_conf.xml file, and restarted Galaxy? see also: http://wiki.galaxyproject.org/**Admin/Tools/Add%20Tool%**20Tutorialhttp://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial Hope this helps Hans-Rudolf On 07/16/2013 08:35 PM, Moritz Juchler wrote: Hello Ladies and Gentlemen, I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to choose a bioinformatic pipeline management tool to find SNP's in genomes from hcc patients. My decision was made in favor of galaxy. I have a 64-bit openSuse 11.3 server. I have installed Galaxy locally, since we have a) very large files (30GB per patient) and b) the data is protection sensitive. I kept close to http://wiki.galaxyproject.org/**Admin/Get%20Galaxyhttp://wiki.galaxyproject.org/Admin/Get%20Galaxy Now I would like to run this bpipe pipeline: http://pastebin.com/sZd5vfdL And the first step is to align my genome to a _hg19 reference genome_ which I have locally under /genedata/human_genome_GRCh37/**. trr@portalmoritz:~ ls -l /genedata/human_genome_GRCh37/ total 8486312 -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa -rw-r--r-- 1 trr root 8591 2013-07-01 16:06 hg19.fa.amb -rw-r--r-- 1 trr root 4040 2013-07-01 16:06 hg19.fa.ann -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05 hg19.fa.bwt -rw-r--r-- 1 trr root 784290318 2013-07-01 16:06 hg19.fa.pac -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31 hg19.fa.sa http://hg19.fa.sa _bwa is installed and gives me:_ trr@portalmoritz:~ bwa Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.5a-r405 Contact: Heng Li l...@sanger.ac.uk mailto:l...@sanger.ac.uk Then I tried to follow this guide: http://wiki.galaxyproject.org/**Admin/NGS%20Local%20Setuphttp://wiki.galaxyproject.org/Admin/NGS%20Local%20Setupto get the reference files and http://wiki.galaxyproject.org/**Admin/Config/Tool%**20Dependencieshttp://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies . This is my _$PATH_ trr@portalmoritz:~ echo $PATH /home/trr/bin:/usr/local/bin:/**usr/bin:/bin:/usr/bin/X11:/** usr/X11R6/bin:/usr/games:/**home/trr/bpipe-0.9.8/bin:/** home/trr/bwa-0.7.5a:/home/trr/**samtools-0.1.19 _In the universe_wsgi.ini I changed:_ tool_dependency_dir = /home/trr/galaxy-dist/tool_**dependency_dir debug = False use_interactive = True library_import_dir = /genedata/ allow_library_path_paste = True admin_users = ... This is my _tool_dependency_dir:_ trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa ls -l total 4 drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4 lrwxrwxrwx 1 trr users6 2013-07-16 14:17 default - 0.7.4/ This is the_version
Re: [galaxy-dev] Cloudman master cannot connect to volume at start-up
Can you verify that the volume does still exist in your account, and that you're launching from the same availability zone that the volume exists in? On Mon, Jul 22, 2013 at 4:13 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: - This is what has been reported by the cluster status log: - - 20:01:14 - Master starting - 20:01:16 - Trouble getting volume reference for volume vol-91cfd1cb: EC2ResponseError: 400 Bad Request**InvalidVolume.NotFound**The volume 'vol-91cfd1cb' does not exist. 9179663c-c5ec-4e90-88ff-ecf606b5e9a6 - 20:01:16 - Attempting to connect to a non-existent volume vol-91cfd1cb - 20:01:16 - Error processing filesystems in existing cluster configuration: 'NoneType' object has no attribute '__getitem__' - 20:01:16 - * Manager failed to start * Any suggestions? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cloudman - is it possible to still use depreciated AMIs ?
Yes, you can still use the deprecated AMIs. What error are you seeing when you try to ssh in? On Mon, Jul 22, 2013 at 4:30 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: I tried launching an instance specifying ami-da58aab3 as the AMI but I am unable to SSH or access Cloudman using the instance's URL. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] CloudMan Error
The warning message printed by the first ssh attempt indicates that you have no cloudman_key_pair.pem in the directory you executed the ssh command from. Find this file (or create a new one) and you'll be able to ssh. Good luck, and please keep threads on the list instead of emailing directly. Thanks! -Dannon On Mon, Jul 22, 2013 at 1:36 PM, deniz...@gmail.com wrote: Hi- the share string appears to be loading, but I am unable to ssh into my instance using the provided command, or anything like it. Instead I get the following: denizerezyilmaz$ ssh -i cloudman_key_pair.pem ubu...@ec2-54-242-61-164.compute-1.amazonaws.com Warning: Identity file cloudman_key_pair.pem not accessible: No such file or directory. OR: denizerezyilmaz$ ssh ec2-54-242-61-164.compute-1.amazonaws.com Permission denied (publickey). What am I missing? Thank you, Deniz ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Running additional services
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.lecl...@aya.yale.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
