Re: [galaxy-dev] first install, MySQL date
On Thu, 28 Feb 2013 13:12:36 -0500 Nate Coraor wrote: Hi Arnau, Hi Nate, The times are intentionally stored in the database in UTC. Times are rarely shown in the interface, but when they are, they should be properly adjusted using the system's currently set timezone. thanks for your reply. Thanks, --nate Cheers, Arnau ___ 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/
Re: [galaxy-dev] Error when upgrading the database to version 110
Hi Derrick This is interesting. we are also using MySQL and I got an error at the same step. However in my case the error message was: (OperationalError) (1050, Table 'repository_repository_dependency_association' already exists) the same was also the case for the repository_dependency table (see below for full error) I have encountered this already several times over then last few years and struggled to understand what was really going on (why is it trying to build the table a second and a third time). Our sysadmins always insisted that there were no other error messages in the MySQL logs. So I ignored it. Knowing your error message, could now explain our situation. (see also below for the index description) So far we have no problems...but we also don't work much with the tool shed. Regards, Hans-Rudolf mysql show index from repository_repository_dependency_association\G *** 1. row *** Table: repository_repository_dependency_association Non_unique: 0 Key_name: PRIMARY Seq_in_index: 1 Column_name: id Collation: A Cardinality: 0 Sub_part: NULL Packed: NULL Null: Index_type: BTREE Comment: *** 2. row *** Table: repository_repository_dependency_association Non_unique: 1 Key_name: tool_shed_repository_id Seq_in_index: 1 Column_name: tool_shed_repository_id Collation: A Cardinality: NULL Sub_part: NULL Packed: NULL Null: YES Index_type: BTREE Comment: *** 3. row *** Table: repository_repository_dependency_association Non_unique: 1 Key_name: repository_dependency_id Seq_in_index: 1 Column_name: repository_dependency_id Collation: A Cardinality: NULL Sub_part: NULL Packed: NULL Null: YES Index_type: BTREE Comment: 3 rows in set (0.00 sec) mysql 108 - 109... Migration script to add the repository_dependency and repository_repository_dependency_association tables. 0109_add_repository_dependency_tables DEBUG 2013-02-26 14:04:55,820 Creating repository_dependency table failed: (OperationalError) (1050, Table 'repository_dependency' already exists) u'\nCREATE TABLE repository_dependency (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, \n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' () 0109_add_repository_dependency_tables DEBUG 2013-02-26 14:04:55,820 Creating repository_dependency table failed: (OperationalError) (1050, Table 'repository_dependency' already exists) u'\nCREATE TABLE repository_dependency (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, \n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER NOT NULL, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' () 0109_add_repository_dependency_tables DEBUG 2013-02-26 14:04:55,821 Creating repository_repository_dependency_association table failed: (OperationalError) (1050, Table 'repository_repository_dependency_association' already exists) u'\nCREATE TABLE repository_repository_dependency_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, \n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER, \n\trepository_dependency_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id), \n\t FOREIGN KEY(repository_dependency_id) REFERENCES repository_dependency (id)\n)\n\n' () 0109_add_repository_dependency_tables DEBUG 2013-02-26 14:04:55,821 Creating repository_repository_dependency_association table failed: (OperationalError) (1050, Table 'repository_repository_dependency_association' already exists) u'\nCREATE TABLE repository_repository_dependency_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME, \n\tupdate_time DATETIME, \n\ttool_shed_repository_id INTEGER, \n\trepository_dependency_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id), \n\t FOREIGN KEY(repository_dependency_id) REFERENCES repository_dependency (id)\n)\n\n' () done On 03/01/2013 05:22 AM, Derrick Lin wrote: Hi guys, I was given the following error when upgrading the database from 109 to 110: 0109_add_repository_dependency_tables DEBUG 2013-03-01 15:14:15,554 Creating repository_repository_dependency_association table failed: (OperationalError) (1059, Identifier name 'ix_repository_repository_dependency_association_tool_shed_repository_id' is too long) u'CREATE INDEX ix_repository_repository_dependency_association_tool_shed_repository_id ON repository_repository_dependency_association (tool_shed_repository_id)' () 0109_add_repository_dependency_tables
[galaxy-dev] Problem with Upload File tool via url
Dear all, My problem is when I use the /Upload File /tool via URL, I get the message The uploaded file contains inappropriate HTML content. I tried a lot of file formats. In our development server this tool works fine but in our public server we have this problem. Do you have any solution? Kind regards, Zinon ___ 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/
Re: [galaxy-dev] Problem with Upload File tool via url
My hunch is that the source location is probably responding with an error page and not the actual content you're looking for. Is the source URL behind any authentication scheme, and can you verify that from, say, curl or wget that it works and responds with the data? -Dannon On Fri, Mar 1, 2013 at 7:16 AM, Zinonas Antoniou z.anton...@gmail.comwrote: Dear all, My problem is when I use the *Upload File *tool via URL, I get the message The uploaded file contains inappropriate HTML content. I tried a lot of file formats. In our development server this tool works fine but in our public server we have this problem. Do you have any solution? Kind regards, Zinon ___ 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/ ___ 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/
Re: [galaxy-dev] Problem with Upload File tool via url
Danno, thank you for your response. Yes, I tried with both curl and wget. They work and they respond with the data. I tried the same file path in test galaxy server (https://test.g2.bx.psu.edu/) and it's working properly. Thanks, Zinon On 1/3/2013 2:53 ??, Dannon Baker wrote: My hunch is that the source location is probably responding with an error page and not the actual content you're looking for. Is the source URL behind any authentication scheme, and can you verify that from, say, curl or wget that it works and responds with the data? -Dannon On Fri, Mar 1, 2013 at 7:16 AM, Zinonas Antoniou z.anton...@gmail.com mailto:z.anton...@gmail.com wrote: Dear all, My problem is when I use the /Upload File /tool via URL, I get the message The uploaded file contains inappropriate HTML content. I tried a lot of file formats. In our development server this tool works fine but in our public server we have this problem. Do you have any solution? Kind regards, Zinon ___ 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/ ___ 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/
Re: [galaxy-dev] [External] Re: macs error for chipseq data
Are you executing `sudo` as the galaxy user, or as the ubuntu user? The galaxy user is not a sudoer, and you shouldn't need to use sudo for anything you want to do as the galaxy user. The only use in this particular case for using `sudo` as root is to switch *to* the galaxy user. -Dannon On Wed, Feb 27, 2013 at 6:34 PM, Sun, Wenping [USA] sun_wenp...@bah.comwrote: Hello, When I sudo galaxy user at ssh terminal, the password prompted for galaxy. What is it? Thanks, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Friday, January 11, 2013 12:12 PM To: Jennifer Jackson Cc: Galaxy Dev; Sun, Wenping [USA] Subject: [External] Re: macs error for chipseq data There's an issue with the MACS installation on the current cloud tools volume (which will be fixed with the next volume update coming soon). For existing instances, you can get MACS working correctly by executing the following two commands (which change the default version of macs used) after ssh'ing in to your instance: sudo su galaxy ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1/mnt/galaxyTools/tools/macs/default And that's it, no need to restart galaxy or anything. -Dannon On Jan 11, 2013, at 10:59 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: Hi Jen, Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out. It seems to me that MACS was installed What is the issue? Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer, Thanks for the information on MACS tools. Yes, I forgot to mention that I used bowtie mapped files as the input. Thank you very much, Kathryn From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data Hello Kathryn, This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 If you need more help with your local install, directing questions to the galaxy-...@bx.psu.edu mailing list would be best, Thanks! Jen Galaxy team On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users, I've encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error An error occurred running this job: /bin/sh: macs: not found Anybody can kindly provide some hints? Thanks, Kathryn ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/
Re: [galaxy-dev] Problem with Upload File tool via url
Glad it worked! Looping this back to the -dev list so that the solution is available for others in the future. -Dannon On Fri, Mar 1, 2013 at 9:00 AM, Zinonas Antoniou z.anton...@gmail.comwrote: Dannon, thank you that was the solution!! We copied the path environment variables from our local to our public server and there was an interference. God bless you! I really appreciate your help!! Kind regards, Zinon On 1/3/2013 3:37 μμ, Dannon Baker wrote: Oh, *your* public server! I misread that completely in your first email, sorry. Are you using a proxy on your main server that might be interfering here? On Fri, Mar 1, 2013 at 8:34 AM, Zinonas Antoniou z.anton...@gmail.comwrote: Weird indeed! Yes, I use the full url. It also works fine in our local development server, but in our public server no. Actually the problem is not only with our url source but with any url source. It seems that when we use the Upload File from url we have the same problem. On 1/3/2013 3:31 μμ, Dannon Baker wrote: Weird, this file works fine for me on main.g2.bx.psu.edu using the normal url upload. Are you pasting in the full url including http:// ? ___ 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/
Re: [galaxy-dev] [External] Re: data from galaxy
I'm a little confused about the state of this instance. In the cloud admin panel, you have a user listed. And, in galaxy, you can log in as that user and act as an admin? But when you go to Manage users there are no users listed? Lastly, I've cc'd galaxy-dev here. Please do try to email the list with these questions, and not individual developers directly. -Dannon On Wed, Feb 27, 2013 at 4:38 PM, Sun, Wenping [USA] sun_wenp...@bah.comwrote: Hi Dannon, I just found that the problem of user and data history from below email that happened again today. The galaxy cloud cluster was terminated 1-2 weeks ago. I have tried once 1 weeks ago to re-launch and it seemed everything was fine, both with users and data history. However, I just tried to re-launch galaxy and found that all the users not there. the admin email still on the galaxy launch page, however, on manage users from galaxy interface, there was no user there (it suppose 2 user, same as the admin I added in the first place). All the data history was not available because of that as well. I really appreciate your help on this at your early convenience!! I need to retrieve them for tomorrow morning meeting. Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Monday, January 21, 2013 9:51 AM To: Sun, Wenping [USA] Subject: Re: [External] Re: data from galaxy Different -- the point is to create a *new* admin user since the password was lost for the other one. On Jan 21, 2013, at 9:50 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Use different email address or the same? -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Monday, January 21, 2013 9:50 AM To: Sun, Wenping [USA] Subject: Re: [External] Re: data from galaxy Add a new user as an admin in the cloudman interface, and then register and log in as that new user. Then look at the Admin section of Galaxy and you can reset the password for your other user there. On Jan 21, 2013, at 9:47 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: No, I tried and it said not recognized. I even cannot reset the password, here is the error for reset password Mail is not configured for this Galaxy instance. Please contact an administrator. I have lot of data and don't have time to reproduce them. Please help me with this. Thanks a lot! Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Monday, January 21, 2013 9:45 AM To: Sun, Wenping [USA] Subject: [External] Re: data from galaxy You should be able to log back in with the same username and password you used before. Is it not working? -Dannon On Jan 21, 2013, at 9:43 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Hi Dannon, I have the whole processed data from galaxy on cloudman and they are on during the weekend. However, I found out that I was logged out this morning. My user name is still in admin. I tried to log in but I could not. This data takes time and would you please direct me how to get back to my data? Thank you in advance! Kathryn ___ 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/
[galaxy-dev] Reloading *.loc files
Hello all, Re: BitBucket Issue 538 - Admin action to reload .loc files without restarting Galaxy https://trello.com/card/538-admin-action-to-reload-loc-files-without-restarting-galaxy/506338ce32ae458f6d15e4b3/475 Currently Galaxy administrators can reload a tool's XML configuration file, which is very helpful (especially as a developer working on changes to a single tool). Similarly it would be useful to be able to reload one (or all) of the *.loc files (e.g. if a new BLAST database is added), without having to restart Galaxy. Further to this, it would be useful to trigger this from a script via the Galaxy API or otherwise. Should this be filed as a new issue, or a comment on the existing issue? Another idea for enhancement would be to monitor the loc files for *automatic* reloading without user or script intervention (but that might be too much magic), or simply (re)loading loc files on demand rather than at startup. Do the Galaxy team have any plans in this area? 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/
Re: [galaxy-dev] [External] Re: data from galaxy
When galaxy instance was launched, I have two user listed as admin on cloud admin panel. However, in galaxy site, I couldn't log in with either user. When I added additional user at cloud panel to access galaxy's admin, in manage users there is no user there. Thanks for the help, Kathryn From: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: Friday, March 01, 2013 9:06 AM To: Sun, Wenping [USA] Cc: Galaxy Dev Subject: Re: [External] Re: data from galaxy I'm a little confused about the state of this instance. In the cloud admin panel, you have a user listed. And, in galaxy, you can log in as that user and act as an admin? But when you go to Manage users there are no users listed? Lastly, I've cc'd galaxy-dev here. Please do try to email the list with these questions, and not individual developers directly. -Dannon On Wed, Feb 27, 2013 at 4:38 PM, Sun, Wenping [USA] sun_wenp...@bah.commailto:sun_wenp...@bah.com wrote: Hi Dannon, I just found that the problem of user and data history from below email that happened again today. The galaxy cloud cluster was terminated 1-2 weeks ago. I have tried once 1 weeks ago to re-launch and it seemed everything was fine, both with users and data history. However, I just tried to re-launch galaxy and found that all the users not there. the admin email still on the galaxy launch page, however, on manage users from galaxy interface, there was no user there (it suppose 2 user, same as the admin I added in the first place). All the data history was not available because of that as well. I really appreciate your help on this at your early convenience!! I need to retrieve them for tomorrow morning meeting. Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.commailto:dannonba...@me.com] Sent: Monday, January 21, 2013 9:51 AM To: Sun, Wenping [USA] Subject: Re: [External] Re: data from galaxy Different -- the point is to create a *new* admin user since the password was lost for the other one. On Jan 21, 2013, at 9:50 AM, Sun, Wenping [USA] sun_wenp...@bah.commailto:sun_wenp...@bah.com wrote: Use different email address or the same? -Original Message- From: Dannon Baker [mailto:dannonba...@me.commailto:dannonba...@me.com] Sent: Monday, January 21, 2013 9:50 AM To: Sun, Wenping [USA] Subject: Re: [External] Re: data from galaxy Add a new user as an admin in the cloudman interface, and then register and log in as that new user. Then look at the Admin section of Galaxy and you can reset the password for your other user there. On Jan 21, 2013, at 9:47 AM, Sun, Wenping [USA] sun_wenp...@bah.commailto:sun_wenp...@bah.com wrote: No, I tried and it said not recognized. I even cannot reset the password, here is the error for reset password Mail is not configured for this Galaxy instance. Please contact an administrator. I have lot of data and don't have time to reproduce them. Please help me with this. Thanks a lot! Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.commailto:dannonba...@me.com] Sent: Monday, January 21, 2013 9:45 AM To: Sun, Wenping [USA] Subject: [External] Re: data from galaxy You should be able to log back in with the same username and password you used before. Is it not working? -Dannon On Jan 21, 2013, at 9:43 AM, Sun, Wenping [USA] sun_wenp...@bah.commailto:sun_wenp...@bah.com wrote: Hi Dannon, I have the whole processed data from galaxy on cloudman and they are on during the weekend. However, I found out that I was logged out this morning. My user name is still in admin. I tried to log in but I could not. This data takes time and would you please direct me how to get back to my data? Thank you in advance! Kathryn ___ 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/
[galaxy-dev] Fwd: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts
Dear all, Apologies if you've already seen the SciPy 2013 conference call. This year's SciPy should be of particular relevance to Python programmers working with Galaxy. There is a new bioinformatics mini-symposium this year (chaired by Brad Chapman who contributes to Galaxy, Biopython, etc), but also a special theme this year on reproducible science which is of course one of the goals of the Galaxy Project. I hope some Galaxy people submit abstracts - although the timing of SciPy 2013 (in Texas USA) just before the Galaxy Community Conference (in Norway) is unfortunate: http://wiki.galaxyproject.org/Events/GCC2013 Regards, Peter -- Forwarded message -- From: Jonathan Rocher jroc...@enthought.com Date: Wed, Feb 27, 2013 at 10:17 PM Subject: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts To: SciPy Users List scipy-u...@scipy.org, numfo...@googlegroups.com, Discussion of Numerical Python numpy-discuss...@scipy.org [Apologies for cross-posts] Dear all, The annual SciPy Conference (Scientific Computing with Python) allows participants from academic, commercial, and governmental organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. The deadline for abstract submissions is March 20th, 2013. Submissions are welcome that address general Scientific Computing with Python, one of the two special themes for this years conference (machine learning reproducible science), or the domain-specific mini-symposia held during the conference (Meteorology, climatology, and atmospheric and oceanic science, Astronomy and astrophysics, Medical imaging, Bio-informatics). Please submit your abstract at the SciPy 2013 website abstract submission form. Abstracts will be accepted for posters or presentations. Optional papers to be published in the conference proceedings will be requested following abstract submission. This year the proceedings will be made available prior to the conference to help attendees navigate the conference. We look forward to an exciting and interesting set of talks, posters, and discussions and hope to see you at the conference. The SciPy 2013 Program Committee Chairs Matt McCormick, Kitware, Inc. Katy Huff, University of Wisconsin-Madison and Argonne National Laboratory ___ NumPy-Discussion mailing list numpy-discuss...@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ 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/
[galaxy-dev] Authentication: email addresses are not validated prior to account creation
Hello members, I believe currently there is no process to validate email address provided during user account creation. We are experiencing a huge fake account creation attack on our public facing galaxy instancehttp://galaxy.raetschlab.org . Does anybody who has been managing a public instance, implemented an on-demand account creation activation by sending an email containing a link, which when clicked, validate the account creation request. Or any plans from dev-team to add this in future release? thanks in advance, --/Vipin ___ 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/
Re: [galaxy-dev] Public ToolShed Problem - Latest Version isn't the tip repo
Hello Fei-Yang, It's not possible to explain the cause of this without knowing to what repository you are referring. Have you tried resetting all metadata on your repository? Greg Von Kuster On Feb 11, 2013, at 11:02 AM, Fei-Yang Jen wrote: Hi Galaxy_dev team, I have question with regards to public ToolShed. For some reason, the latest version of my tools didn't get picked as tip repo when I was trying to install it on my cloud instance. I have read about some unexpected behaviours of public ToolShed if I use it like a git repo. Without knowing that at the first place, I had been modifying my tools on public ToolShed and had multiple uploads of some files. Is it possible that this is the reason why the latest version of my upload doesn't get picked as a tip repo? If it is so, how can I go about to fix it ? (I was looking for a way to delete repositories, but there didn't seem to have one) Thanks, Fei-Yang (Arthur) Jen Student Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ___ 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/ ___ 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/
Re: [galaxy-dev] blend4j
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Marc Logghe
Sent: Thursday, February 28, 2013 10:25 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] blend4j
Hi all,
Is this the correct forum to post blend4j issues ? Apologies if this is not the
case.
I was trying to run a custom workflow via blend4j, according to
https://github.com/jmchilton/blend4j
In my hands, the call to workflowDetails.getInputs() returns an empty Map. I
believe the corresponding REST request looks like:
/galaxy/api/workflows/workflow id?key=API key
In the JSON response, the 'inputs' attribute is empty indeed ({url:
/galaxy/api/workflows/f09437b8822035f7, inputs: {}, ...).
I do not understand why this is the case because 2 steps require inputs to be
set at runtime. Via the Galaxy web interface those required parameters can be
set and the workflow is running smoothly.
Or has the term 'inputs' nothing to do with 'parameters' ?
Please allow me to come back to this. I now realize that the workflow needs 2
inputs (instead of parameters). As far as I understand, for the moment it is
not possible to pass parameter values via the REST API without tempering with
the JSON strings themselves.
But dataset inputs should be supported. In my case, step 1 and step 2 need the
same dataset as input.
According to this snippet taken from the blend4j page (shown below), the
workflow should provide you with the input ids (here workflowInput1Id and
workflowInput2Id).
The issue is I don't have a clue what these input ids are, since in my hands
workflowDetails.getInputs() returns an empty collection. Do you need to add
metadata/attributes to the workflow in order to have these input IDs returned ?
final WorkflowDetails workflowDetails =
workflowsClient.showWorkflow(matchingWorkflow.getId());
String workflowInput1Id = null;
String workflowInput2Id = null;
for(final Map.EntryString, WorkflowInputDefinition inputEntry :
workflowDetails.getInputs().entrySet()) {
final String label = inputEntry.getValue().getLabel();
if(label.equals(WorkflowInput1)) {
workflowInput1Id = inputEntry.getKey();
}
if(label.equals(WorkflowInput2)) {
workflowInput2Id = inputEntry.getKey();
}
}
final WorkflowInputs inputs = new WorkflowInputs();
inputs.setDestination(new
WorkflowInputs.ExistingHistory(matchingHistory.getId()));
inputs.setWorkflowId(matchingWorkflow.getId());
inputs.setInput(workflowInput1Id, new
WorkflowInputs.WorkflowInput(input1Id, WorkflowInputs.InputSourceType.HDA));
inputs.setInput(workflowInput2Id, new
WorkflowInputs.WorkflowInput(input2Id, WorkflowInputs.InputSourceType.HDA));
final WorkflowOutputs output = workflowsClient.runWorkflow(inputs);
System.out.println(Running workflow in history + output.getHistoryId());
for(String outputId : output.getOutputIds()) {
System.out.println( Workflow writing to output id + outputId);
}
Regards,
Marc
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[galaxy-dev] Search software on public Galaxy servers
Hi community, Due to the increasing Galaxy public servers PublicGalaxyServershttp://wiki.galaxyproject.org/PublicGalaxyServers it would be very useful to have a search tool in order to look for software ready-to-use in the public servers. Since I know this is not available. Will it be feasible? Here is the Trello Card https://trello.com/c/FdF5h17c Regards, Bernardo -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es * * * ___ 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/
[galaxy-dev] Bug in gene expression index
I am using galaxy main user name opsms problem: correctly uploaded data are not visible in the box under file set chosen from your history This was noted at 3.30pm 27 Feb 2013 - This is what I did 1.uploaded zipped CEL files. --- these were seen in history 2.Clicked Gene expression 3.Then expression index -- This is as far as I got: Gene expression index (version 1.0.0) Operation Type: Title to label the new output file: File set chosen from your history: Choose a CEL/XYS file archive from your current history Please help! Sri Srilakshmi___ 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/
[galaxy-dev] Datatype dropdown only 8px wide
Hello, I am having a slight issue with the Datatype tab of the edit page. I am using a locally installed version of galaxy-dist obtained from bitbucket. I cannot see anything in the dropdown menu to change the datatype. According to the HTML, the box is only 8px wide. div class=select2-container id=s2id_autogen2 style=width: 8px Is there any way to fix this problem without having to re-install galaxy? Thanks, Kelvin ___ 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/
[galaxy-dev] cuff configure
I have a local install of Galaxy. Tophat2 and Cufflinks work. cuffcompare and cuffmerge do not. Errors are below. There isn't a .loc file for cufflinks (overall). It will run if I don't 'use sequence'. It appears that the name of the database (dbkey) is inherited from the Tophat2 output file, but it coming up empty for cuff compare and cuffmerge. Any thoughts how I can get this to work? An error occurred running this job: *cuffcompare v2.0.2 (3524M) No sequence data found for dbkey ?, so sequence data cannot be used. cp: /Users/galaxy/galaxy-dist/database/job_working_directory/001/1549/cc_output.input1.tmap: No such file or directory cp: /Users/galaxy/galaxy-dist/database/j* * * * * ___ 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/
