[galaxy-dev] multiple file selection for from_file
Hi all I gather that it is NOT allowed to assign multiple file to from_file attribute for options in select param as the expect value of from_file attribute is the name of A file. But would it be nice to allow this feature? For example, there are two loc file A and B, when I want to get the options from both files, instead of adding an extra file containing all options from two files, it will be more maintainable to use something like from_file = A.loc, B.loc, isn't it? BTW, could anyone help me on this http://dev.list.galaxyproject.org/jobs-don-t-get-killed-when-histories-deleted-tc4664678.html? Best regards! Jun ___ 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] jobs don't get killed when histories deleted
Hi all, It seems that this problem has been reported before http://dev.list.galaxyproject.org/jobs-don-t-get-killed-when-histories-deleted-tp4658452.html and should be solved https://trello.com/card/jobs-stop-job-function-in-jobs-admin-interface-is-broken/506338ce32ae458f6d15e4b3/627. However I am using the Apr-2014 version (at least the version with the fancy Load Data button at top of tools panel which is a quite new feature). The jobs from deleted histories still hang around in the manage jobs admin page with some cannot-finish setting_metadata jobs. The interesting thing is that the last update time is always less than 24 hours. How to delete these unwanted jobs? Best regards! Jun ___ 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] complex help for conditional param
Hi all, In the conditional param, when sub-element allows you to write specific parameters for a particular value selected. I am wondering how to write the help context according to the value selection. For example, if there is a conditional param called blast_type, when blastn is selected, the help context will be blast dna against dna and when blastp is selected, the help context will be blast protein against protein. Basically this selection-based help text provides a general description of the selection, which could help to set up the corresponding parameters. By the way, is there any document about formatting text in the help element? Best regards! Jun ___ 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] complex help for conditional param
Hi Peter, I am afraid that the link you gave me could not solve the problem. The question I asked is about the help element, not the label attribute for data element. To clarify my question, here is the code which does not work, but shows what I intend to do: conditional name=blast param name=type type=select label=BLAST type option value=blastnBLASTN/option option value=blastpBLASTP/option /param when value=blastn helpBLAST DNA against DNA/help param... /when when value=blastp helpBLAST protein against protein/help param... /when /conditional I tried to set the help content according to the selected type, which works like a section header to the following param list. Obviously this does not work. Then I tried a less-fancy way by providing static help context by adding help under select param like param name=type type=select label=BLAST type helpBLASTN: BLAST DNA against DNA, BLASTP: BLAST protein against protein/help option value=blastnBLASTN/option Of course it works but in an ugly formatting text. Is there any document to format it nicely, e.g. a list? Best regards! Jun -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: Tuesday, May 27, 2014 4:40 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] complex help for conditional param On Tue, May 27, 2014 at 4:32 PM, Jun Fan j@qmul.ac.uk wrote: Hi all, In the conditional param, when sub-element allows you to write specific parameters for a particular value selected. I am wondering how to write the help context according to the value selection. For example, if there is a conditional param called blast_type, when “blastn” is selected, the help context will be “blast dna against dna” and when “blastp” is selected, the help context will be “blast protein against protein”. Basically this selection-based help text provides a general description of the selection, which could help to set up the corresponding parameters. By the way, is there any document about formatting text in the help element? Best regards! Jun You can do this kind of thing with one-line Cheetah syntax within the output XML tag, but it quickly gets very complicated. e.g. https://github.com/peterjc/pico_galaxy/commit/3991893c6ee2cc69c33aaa391bbed412c85fa9db 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] dynamic number of outputs in workflow context
Dear all, I have a tool which generates dynamic number of mzid outputs depending on the number of selected files and tools ( = number of files * number of tools). The suggested methods to deal with this situation are 1) composite html which contains links to all outputs or 2) put output files in the $__new_file_path__ with some naming convention. Neither of these can specify the output type of the tool to the desired value mzid, which makes it impossible to connect this tool to the downstream tool taking mzid as input. My solution to this is to limit to single file selection, then listing all possible mzid output files with filter elements. I am wondering whether there is better solution to solve this. Another question about workflow: if a tool A can generate two types of output: C and D, and another tool B can take type C, D and E as its input, it is fine to connect these two tools A and B in the workflow. However, if the types selected for input and output do not match (e.g. type C for tool A output and type D for tool B input or even type E), how to configure galaxy to spot this inconsistency? Best regards! Jun ___ 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] apache setting
Hi Carlos, It worked perfectly last time. But now on the new Ubuntu 14.04, no file called default exists under the folder sites-available, instead there are two files: 000-default.conf and default-ssl.conf. From the content of the files, 000-default.conf is more likely to be the alternative. I inserted directives as before and restart the apache service. The web browser told me that “Permission denied” even the galaxy-dist folder and its subfolder have at least 744 permission (everyone should be able to read). How can I solve this “Permission denied” issue? Best regards! Jun From: Carlos Borroto [mailto:carlos.borr...@gmail.com] Sent: Tuesday, March 25, 2014 3:45 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] apache setting On Monday, March 24, 2014, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] I tried to add them to 1) the main conf file: apache2.conf, 2) newly generated httpd.conf by myself under /etc/apache2 folder and 3) newly generated .htaccess file under /etc/apache2/conf.d folder, and none of them gave me the luck. This thread might help you: http://dev.list.galaxyproject.org/Running-Galaxy-behind-apache2-td4624545.html --Carlos ___ 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] user account activation
Hi Dan, It solves the problem, thanks! Regards! Jun From: Daniel Blankenberg [mailto:d...@bx.psu.edu] Sent: Monday, May 12, 2014 5:49 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account activation Hi Jun, Do you also have require_login = True, set in your universe_wsgi.ini? That will disable anonymous access. Thanks for using Galaxy, Dan On May 10, 2014, at 8:44 PM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Dear all, Has anyone got the problem of enabling user account activation recently? In the past, after setting user_activation_on = True in the universe_wsgi.ini, when I click Analyze Data, a login window will appear to force me to log in. Now I can upload file without login and the green status showed in the history. When I tried to register a new user, the grey status of the upload tool appeared. I did receive the activation email. Best regards! Jun ___ 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/
[galaxy-dev] user account activation
Dear all, Has anyone got the problem of enabling user account activation recently? In the past, after setting user_activation_on = True in the universe_wsgi.ini, when I click Analyze Data, a login window will appear to force me to log in. Now I can upload file without login and the green status showed in the history. When I tried to register a new user, the grey status of the upload tool appeared. I did receive the activation email. Best regards! Jun ___ 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] user account
Hi Martin, Thanks for the tip of changing email and username under SQL. I managed that (update galaxy_user set email=’h...@haha.com’, username=’haha’ where id = NNN) and tried to re-register with the same email. Then I got some error saying “Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. “ Also the link in the verification email does not do the job. Anyway, I used the SQL again to bypass this issue (active=’t’, activation_token=’’) Problem solved. Many thanks for your help. Best regards! Jun From: emulato...@gmail.com [mailto:emulato...@gmail.com] On Behalf Of Martin Cech Sent: Friday, April 25, 2014 5:05 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account Hi Jun, Galaxy does not really delete users. If you are trying to clear the user, just change its email as an admin and register the user again with the same address as before. Martin On Thu, Apr 24, 2014 at 8:56 PM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi Martin, Thanks for the hint. After setting track_jobs_in_database to True, the status of the new upload is waiting to run, which should be the behavior expected. Luckily when I modified the setting in universal_wsgi.ini, I noticed that there is an option allow_user_deletion = True which enables the user deletion in UI. The problem is that even I deleted and purged one email, I still can re-register with that email. What is the solution to this? Direct SQL operation? Best regards! Jun From: emulato...@gmail.commailto:emulato...@gmail.com [mailto:emulato...@gmail.commailto:emulato...@gmail.com] On Behalf Of Martin Cech Sent: Thursday, April 24, 2014 9:50 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account Hi Jun, the account activation is meant for multi-processor environments and these have to have the following option turned on in the configuration: track_jobs_in_database = True Please try to change it. thank you Martin On Thu, Apr 24, 2014 at 4:27 PM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi Martin I am using Postgresql. Best regards! Jun From: emulato...@gmail.commailto:emulato...@gmail.com [mailto:emulato...@gmail.commailto:emulato...@gmail.com] On Behalf Of Martin Cech Sent: Thursday, April 24, 2014 5:21 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account Hi Jun, what kind of database are you using? This feature might not be supported for SQLite (as no production Galaxy should run on it :)) best Martin Galaxy Team On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for “operations.append” and “item.deleted” and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make “delete user” function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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/
[galaxy-dev] user account
Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for operations.append and item.deleted and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make delete user function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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] user account
Hi Martin I am using Postgresql. Best regards! Jun From: emulato...@gmail.com [mailto:emulato...@gmail.com] On Behalf Of Martin Cech Sent: Thursday, April 24, 2014 5:21 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account Hi Jun, what kind of database are you using? This feature might not be supported for SQLite (as no production Galaxy should run on it :)) best Martin Galaxy Team On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for “operations.append” and “item.deleted” and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make “delete user” function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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] user account
Hi Martin, Thanks for the hint. After setting track_jobs_in_database to True, the status of the new upload is waiting to run, which should be the behavior expected. Luckily when I modified the setting in universal_wsgi.ini, I noticed that there is an option allow_user_deletion = True which enables the user deletion in UI. The problem is that even I deleted and purged one email, I still can re-register with that email. What is the solution to this? Direct SQL operation? Best regards! Jun From: emulato...@gmail.com [mailto:emulato...@gmail.com] On Behalf Of Martin Cech Sent: Thursday, April 24, 2014 9:50 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account Hi Jun, the account activation is meant for multi-processor environments and these have to have the following option turned on in the configuration: track_jobs_in_database = True Please try to change it. thank you Martin On Thu, Apr 24, 2014 at 4:27 PM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi Martin I am using Postgresql. Best regards! Jun From: emulato...@gmail.commailto:emulato...@gmail.com [mailto:emulato...@gmail.commailto:emulato...@gmail.com] On Behalf Of Martin Cech Sent: Thursday, April 24, 2014 5:21 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] user account Hi Jun, what kind of database are you using? This feature might not be supported for SQLite (as no production Galaxy should run on it :)) best Martin Galaxy Team On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for “operations.append” and “item.deleted” and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make “delete user” function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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/
[galaxy-dev] label element
Hi all, It seems that the recent release does not support label element anymore, i.e. no sub-section with the section title displayed in grey. Is there any alternative way to organize the tool under one big section? Best regards! Jun ___ 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] apache setting
Hi all, Following the instruction on https://wiki.galaxyproject.org/Admin/Config/ApacheProxy to use Apache as proxy for Galaxy, I got stuck to put directives into the configuration file. The steps I took include: 1. install apache2: sudo apt-get install apache2 2. install modules mod_proxy, mod_http_proxy and mod_rewrite to support proxying a. check if mod are already enabled using: apache2ctl -M b. install: sudo a2enmod rewrite, sudo a2enmod proxy, sudo a2enmod proxy_http 3. give galaxy permission to the apache user a. find out the user who runs apache: ps -ef | grep apache and find out it is www-data b. find out groups galaxy belong: groups galaxy = galaxy c. add user www-data to group galaxy: sudo usermod -a -G galaxy www-data I believe that I have completed the job required above the Basic configuration section. I tried the first example: RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] I tried to add them to 1) the main conf file: apache2.conf, 2) newly generated httpd.conf by myself under /etc/apache2 folder and 3) newly generated .htaccess file under /etc/apache2/conf.d folder, and none of them gave me the luck. I used sudo service apache2 restart after every time I tried. There is a warning Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName. When I type the address 127.0.0.1 or 127.0.1.1, both of them only gave me the default apache home page, not the Galaxy page. Of course the Galaxy is running on the same server. Could anyone give me some clue to continue? Best regards! Jun ___ 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] . Output file to history (Sebastian Luna Valero)
Hi Sebastian, I am not an expert in galaxy developing. So the following content is just my personal opinion. I do not think it is possible to meet you requirement. I reckon Galaxy searches the certain folder, defined in the universal_wsgi.ini by a parameter called #collect_outputs_from = new_file_path,job_working_directory. On top of that, a job id is required, which is the reason in the dynamic multiple output job id is part of the file name. If your script.py cannot follow the rules, Galaxy for sure cannot recognize the outputs. Normally in this kind of case, I write an additional script to execute the script.py with its original parameter and do the file manipulation afterwards. Of course this is not ideal, but I do nothing about python. It may be possible to write some complicated python code within the command tag of your wrapper file to do this. I am here also waiting for experts' opinions/comments. Best regards! Jun On 3/21/14 9:28 AM, Sebastian Luna Valero wrote: Dear All, I am trying to add a new tool in Galaxy and I have the following problem. Let me explain a simplified example. Let's imagine that my script works from CLI as follows: python script.py --input input-file --pattern output-pattern After processing input-file, the script writes several output files and their name is given according to output-pattern. The number of output files depends on the content of input-file. The output files are written to the current working directory where script.py is located. In the simplest scenario, I get only one output file in the working directory. My problem is that I would like to see the output files in Galaxy's history without modifying the CLI interface. To solve this problem, I have looked at the wiki page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#N umber_of_Output_datasets_cannot_be_determined_until_tool_run and the email here: http://dev.list.galaxyproject.org/Multiple-output-files-do-not-appear- in-history-td4660470.html However, I think that mine is a different scenario. I do not want to add new output parameters in the CLI. I would like Galaxy to bring these output files to my history without modifying the CLI options, is that possible? Many thanks in advance for your help! Best regards, Sebastian. ___ 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] migrate to postgresql
Hi Cesar, I have tried different combinations of setting: 1. The default setting, the service can start, but galaxy cannot connect to local all all ident host all all 127.0.0.1/32 ident host all all ::1/128 ident 2. the working setting on the Ubuntu machine (pgsql 9.1), but on CentOS, the service cannot start local all all peer host all all 127.0.0.1/32 md5 host all all ::1/128 md5 3. The setting I used to test the new created pgsql user and password under command line. Yes, the password is required under command line as planned local all postgres ident local all all md5 host all all 127.0.0.1/32 ident host all all ::1/128 ident 4. Your suggestion works magically local all all ident host all all 127.0.0.1/32 ident host all all ::1/128 ident I cannot thank you enough for this simple but magical tip, before which I never thought about to change host lines as local word is so attempting to set anything for localhost in that line. Best regards! Jun From: César Acevedo [mailto:ing.cesaracev...@gmail.com] Sent: Friday, March 21, 2014 1:37 PM To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] migrate to postgresql Jun, You need to change the value of host in pg_hba.conf from ident to trust and then start your psql service Regards. CA On Thu, Mar 20, 2014 at 3:04 AM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi all, I followed the instruction on https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer and managed to migrate to a postgresql on a Ubuntu machine. However when I tried on a CentOS 6.5, it failed.The steps are: 1. Create psql user galaxy: under psql prompt, a. CREATE USER galaxy WITH PASSWORD 'galaxy'; b. CREATE DATABASE galaxy; c. GRANT ALL PRIVILEGES ON DATABASE galaxy to galaxy; 2. test the created account: change authentication method to password in pg_hba.conf and the username/password works 3. add postgresql://galaxy:galaxy@localhost/galaxy to universal_wsgi.ini 4. sh run.sh gave me the error saying FATAL: Ident authentication failed for user galaxy 5. even I changed back to the default IDENT authentication for postgresql in pg_hba.conf, the same error message appeared. Could anyone help me to spot the error here? Best regards! Jun ___ 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/
[galaxy-dev] migrate to postgresql
Hi all, I followed the instruction on https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer and managed to migrate to a postgresql on a Ubuntu machine. However when I tried on a CentOS 6.5, it failed.The steps are: 1. Create psql user galaxy: under psql prompt, a. CREATE USER galaxy WITH PASSWORD 'galaxy'; b. CREATE DATABASE galaxy; c. GRANT ALL PRIVILEGES ON DATABASE galaxy to galaxy; 2. test the created account: change authentication method to password in pg_hba.conf and the username/password works 3. add postgresql://galaxy:galaxy@localhost/galaxy to universal_wsgi.ini 4. sh run.sh gave me the error saying FATAL: Ident authentication failed for user galaxy 5. even I changed back to the default IDENT authentication for postgresql in pg_hba.conf, the same error message appeared. Could anyone help me to spot the error here? Best regards! Jun ___ 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] LWR questions
Hi John,
Thanks for your reply.
Question 1:
I used the relative path (e.g. ../../../applications/executable) which
still does not work. I have managed to put the script in the same folder which
works though against the initial design.
Question 2:
I pass the $output to the perl script within which a file is generated
with the filename contained in $output. The Galaxy server can recognize the
output. However when I generate another file with the name
primary_$job.id_additional_visible_txt in the same folder as the $output. In
theory, it should also be recognized by Galaxy as being in the
job_working_directory. But it is not. Could you reckon the reason?
Question 3:
Your explanation is very clear. Thank you again for this. The initial
purpose of asking this question is related to question 2: I was wondering which
correct folder I should use to put the additional optional outputs. Now as
you suggested, I should not worry about it at all.
Question 4:
I have managed to convert a RAW file (900M) to mzML (2.3G). But if there
is a limit on the file size, the spectral file maybe need to be split into
multiple mgf files.
Best regards!
Jun
-Original Message-
From: John Chilton [mailto:jmchil...@gmail.com]
Sent: Monday, March 3, 2014 2:27 PM
To: Jun Fan
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] LWR questions
Hey Jun,
Thanks for your continued interest in the LWR. Responses inline.
On Sun, Mar 2, 2014 at 7:00 PM, Jun Fan j@qmul.ac.uk wrote:
Hi all,
LWR sounds very attractive and promising. However how to program
on galaxy side to utilize LWR server is not thoroughly documented.
Critique noted, I have tried to make it seamless but when you move a job from
Linux to Windows there are bound to be severe limitations and I should document
these more clearly and provide a guide for writing Windows compatible tools
(https://bitbucket.org/jmchilton/lwr/issue/9/provide-documentation-for-writing-windows).
I have
several questions to ask:
1. I separate the tool wrappers (.xml) and the applications (.pl, .py
etc) in two different folders. In the traditional way it works fine.
When I use the legacy way of using LWR (adding galaxy:tool_runners
section in the universal_wsgi.ini file), the error message says that
the application cannot be found. Does the executable have to be in the
same folder with the wrapper?
Do you hard code absolute paths to your scripts in the tool XML files then? The
LWR does not support that. If you place a single script in the same folder as
the XML (a simple light-weight wrapper as is fairly
common) - that is supported - otherwise you will need to place all the required
dependencies on the LWR's path on the remote Windows server.
This could get awkward if used with interpreter tag for instance - if you send
me examples of your tools I can provide some guidance.
I guess in general my advice for Windows tools would be if you can use a simple
one-file wrapper script placed next the tool you are fine - just make sure the
underlying application is loaded from the path instead of via absolute paths -
and then make sure all dependencies for the wrapper script are installed on the
remote server and the underlying application is on the LWR's path.
(If your remote server is a *nix server there is new support for using
tool_dependency_dir style Galaxy dependencies that resolve on the remote server
- but this will not work with Windows (enhancements to provide this would be
welcomed though) ).
2. In the thread
http://dev.list.galaxyproject.org/Managing-Data-Locality-td4662438.htm
l#a4662570 John only mentioned $GALAXY_ROOT/databases/files, does this
mean that the dynamic multiple output is not supported as it uses
$GALAXY_ROOT/databases/tmp folder?
https://bitbucket.org/galaxy/galaxy-central/src/eafb4208db665dfeed7d8f3e6f0d2b61ce2f4fc8/universe_wsgi.ini.sample?at=default#cl-213
My understanding is that writing those files to the databases/tmp is somewhat
deprecated - ideally these should be written to the working directory of the
job. The newest version of the LWR *should* attempt to transfer various kinds
of working directory files back to the Galaxy server after the job is complete
- these files *should* include such variable output files. This hasn't been
tested on Windows though
- if there are problems please let me know and I can try to address them -
https://bitbucket.org/jmchilton/lwr/src/51f097d3d517064159bd959c61cee71f7894ea92/lwr/lwr_client/staging/down.py?at=default#cl-17
3. What types of files are supposed to be stored under tools directory
(tool_files), working directory (working), inputs (inputs), configs
directory (configs), all of which are subfolders of
${staging_directory}/${job_identifier}?
In theory, you shouldn't need to be worried about these implementations details
as an application programmer, it should feel just like Galaxy (again
[galaxy-dev] LWR questions
Hi all,
LWR sounds very attractive and promising. However how to program on
galaxy side to utilize LWR server is not thoroughly documented. I have several
questions to ask:
1. I separate the tool wrappers (.xml) and the applications (.pl, .py
etc) in two different folders. In the traditional way it works fine. When I use
the legacy way of using LWR (adding galaxy:tool_runners section in the
universal_wsgi.ini file), the error message says that the application cannot be
found. Does the executable have to be in the same folder with the wrapper?
2. In the thread
http://dev.list.galaxyproject.org/Managing-Data-Locality-td4662438.html#a4662570
John only mentioned $GALAXY_ROOT/databases/files, does this mean that the
dynamic multiple output is not supported as it uses $GALAXY_ROOT/databases/tmp
folder?
3. What types of files are supposed to be stored under tools directory
(tool_files), working directory (working), inputs (inputs), configs directory
(configs), all of which are subfolders of
${staging_directory}/${job_identifier}?
4. Is there file size limit on the LWR server?
Best regards!
Jun
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Re: [galaxy-dev] multiple output tool in workflow
Hi Jen
Thanks for your reply. Yes, it is my own tool.
The outputs element is
outputs
data format=gff3 name=output/
/outputs
In the command element, the three output files are defined as below
$output /$__new_file_path__/primary_${output.id}_samWithPeptides_visible_sam
/$__new_file_path__/primary_${output.id}_longestORFs_visible_fasta
Is there anything wrong here?
Best regards!
Jun
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: 09 November 2013 01:05
To: Galaxy Dev
Cc: Jun Fan
Subject: multiple output tool in workflow
Hi Jun,
There is probably a problem with the tool design itself, but that may be what
you are asking how to solve. I wouldn't think this is a problem with workflows
at first pass.
Is this your own tool? Or a tool from the tool shed (the repo developer is
usually the one to make changes, unless you want to try)?
This is the primary tool development wiki, the output tag set is where I
would double check the tool first.
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
I am moving this over to the
galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu mailing list since it is a
tool development question.
Jen
Galaxy team
On 11/8/13 10:19 AM, Jun Fan wrote:
Hi all,
I am trying to creating a workflow from history. One of the tool used
generates multiple outputs in the format of gff3, fasta and sam. Gff3 will be
visualized in IGV and the fasta file is doing further BLAST analysis. Now the
problem is that the automatically generated workflow does not connect the
having-multiple-output tool and the BLAST tool. I failed even I tried to
connect these two tools in the workflow by hand. I am guessing this is due to
only the main output type (gff3) is recognized in the workflow. How could I
solve this problem?
Best regards and have a nice weekend!
Jun
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Re: [galaxy-dev] pass regular expression
Hi Ross, Thank you very much for guiding me to use sanitize tag. I searched the forum and found this post extremely helpful http://gmod.827538.n3.nabble.com/preserving-newlines-in-input-parameters-td4022647.html. The problem got solved at least for now. One more question: is there anything like predefined set for all special characters, something like string.letters, string.digits ? Otherwise I have to define each of them in the add and remove list. Best regards! Jun From: Ross [mailto:ross.laza...@gmail.com] Sent: 26 October 2013 03:07 To: Jun Fan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] pass regular expression Hi, Jun. The inbuilt parameter sanitizer can be controlled - see http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set The valid sub-tag allows precise control and you can specify eg string.printable if you want ANY printable character in your parameter Here's an example from the Tool Factory: param name=tool_name type=text value=My dynamic script label=New tool ID and title for outputs size=60 help=This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with$ sanitizer invalid_char= valid initial=string.letters,string.digits/ /sanitizer /param I hope this helps? On Sat, Oct 26, 2013 at 11:43 AM, Jun Fan j@qmul.ac.ukmailto:j@qmul.ac.uk wrote: Hi all, I am trying to develop a tool which allows the user to use regular expression to only keep the lines matching the given pattern in the output. There are many special characters, e.g. \ in \d. In the perl script the wrapper invokes, the regular expression is printed as Xd+ for the regular expression \d+. My question is how to pass these special characters including \, (, ), ^ etc. correctly into the perl script. Best regards! Jun ___ 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/
[galaxy-dev] pass regular expression
Hi all, I am trying to develop a tool which allows the user to use regular expression to only keep the lines matching the given pattern in the output. There are many special characters, e.g. \ in \d. In the perl script the wrapper invokes, the regular expression is printed as Xd+ for the regular expression \d+. My question is how to pass these special characters including \, (, ), ^ etc. correctly into the perl script. Best regards! Jun ___ 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] outputs label attribute
Dear all, I have managed to use something like outputs data format=fasta name=output label=#echo os.path.splitext (str ($input.name))[0]#-ORF.fasta/ /outputs to display the wanted label for the dataset in the history. However when I applied the same code to other tool wrappers, some weird things happened: the wrapper can still be loaded in the web page, but when I click the execute button to submit the job, nothing happened except the web browser giving the status wait for localhost. I cannot think of any reason for that. The main difference I can think of between the successful wrapper and the failed ones is that in the failed ones I have to do some file manipulations as galaxy always stores its dataset with the file suffix .dat which is not acceptable in the tool, e.g. proteowizard. I have to rename it with the correct suffix and move the final result to the output file. Additional related questions: 1. How to display the selected value of a conditional element in the label? $conditional.value? 2. How to display different strings according to the conditional selection? Similar to command element to use #if #elsif #end if? 3. When usingdata name=output format=csv change_format when input=type value=html format=html/ /change_format /data, could I use label attribute in the data and when elements? Look forward to your kind answers. Many thanks in advance. Best regards! Jun ___ 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] how to generate a workflow with customized tool names
Dear all, I have a tool which contains the function A,B, and C, the output of the function is the input of another function. I have developed a wrapper for this tool using conditional tag to allow users select the function they want. The label of the outputs (datasets) can be defined by label attribute in the outputs. So far so good. However, when I tried to create a workflow from history, the three steps (functions) from the tool are labeled with the same text (the title of the wrapper). My question is how to customize it, e.g. function_A_tool_name, function_B_tool_name which clearly tell the users which function is used instead of the need to check the parameter setting. Best regards! Dr Jun Fan Postdoctoral Researcher School of Biological and Chemical Sciences Queen Mary University of London ___ 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/
