[galaxy-dev] A job is stuck in queue
Hello, I am working with galaxy for a bioinfomatics class at Umass Amherst. I have tried doing the http://manuals.bioinformatics.ucr.edu/home/gui-ngs-analysis tutorial. I am currently on the quality control section trying to use the illumina human data set and the NGS mapping bowtie for illumina program. I enter all of the parameters and hit execute and the job sit in the history/job queue waiting to for the job to run and never runs. What can i do to fix this?? Thanks for your help ~Colin ___ 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] MarkupSafe cannot be fetched
Hello, After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning: /WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/ In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, Visualization menu is absent and I think it should be related to the previous warning? How to ensure that eggs be properly fetched? Thank you in advance, Sarah Maman ___ 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] ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file
It seems like GATK authors at Broad really really want you to phone home every time you use their software. I'm getting this error while running the lastest version: ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for more information and instructions on how to obtain a key. From the Phone_home wiki page: How to Obtain a GATK Key To obtain a GATK key, email gsah...@broadinstitute.org with the subject line GATK Key Request. In your email, please provide us with the reason(s) you need to run the GATK with the phone-home feature disabled. Please be as explicit as possible about why you cannot participate in the phone home feature. Note that the key you will be issued is linked to the email address you used to contact us. In general I don't have an issue with phone home features from software providers I trust, and I do completely trust The Broad Institute. Although, this does sound a little draconian how is being imposed. Nevertheless, I would like to ask for an easier way to deactivate the use of -et NO_ET on Galaxy GATK's wrappers. Right now I'm manually commenting the relevant line, but I think this means my mercurial repository won't get any update from upstream, or that I will have to deal with merging. Regards, 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/
[galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein __**_ 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] MarkupSafe cannot be fetched
On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote: Hello, After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning: /WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/ Hi Sarah, I'm guessing that you are using a cluster with Galaxy. If this is correct, please try the following: 1. Log in to a cluster node as the user that runs Galaxy 2. cd to the galaxy-dist directory 3. run `python ./scripts/fetch_eggs.py` This should grab any missing eggs. In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, Visualization menu is absent and I think it should be related to the previous warning? See the 'enable_tracks' setting in universe_wsgi.ini to enable the Visualization menu. --nate How to ensure that eggs be properly fetched? Thank you in advance, Sarah Maman ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
I'm interested On Apr 27, 2012, at 3:14 PM, Ryan Golhar wrote: This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edumailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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/ -- Brad Langhorst langho...@neb.commailto:langho...@neb.com 978-380-7564 ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
Cool idea. I am very interested in it. One question: how could we attend the conference since we all at different place? Cheers, Tyler On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein __**_ 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/ ___ 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] [Newsletter] Re: Interested in speaking with other institutions deploying Galaxy locally?
JAX would be interested in this. Dave From: Ryan Golhar ngsbioinformat...@gmail.commailto:ngsbioinformat...@gmail.com Date: Friday, April 27, 2012 3:14 PM To: Ann Black-Ziegelbein annbl...@eng.uiowa.edumailto:annbl...@eng.uiowa.edu Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: [Newsletter] Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? This is a great idea. On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edumailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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/ The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
Thanks everyone! Glad to find some common interest. I will see if I can arrange an initial call. Hi Tyler - I was hoping we could just do a voice conference call. It would be great to meet those face to face at the Galaxy Conference in Chicago if some are attending. Thanks! Ann On 4/27/2012 3:07 PM, JIE CHEN wrote: Cool idea. I am very interested in it. One question: how could we attend the conference since we all at different place? Cheers, Tyler On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian mheyd...@jhmi.edu mailto:mheyd...@jhmi.edu wrote: Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu mailto:annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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/ ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
I'm interested too. On 27 Apr 2012, at 21:13, Ann Black-Ziegelbein wrote: Thanks everyone! Glad to find some common interest. I will see if I can arrange an initial call. Hi Tyler - I was hoping we could just do a voice conference call. It would be great to meet those face to face at the Galaxy Conference in Chicago if some are attending. Thanks! Ann On 4/27/2012 3:07 PM, JIE CHEN wrote: Cool idea. I am very interested in it. One question: how could we attend the conference since we all at different place? Cheers, Tyler On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian mheyd...@jhmi.edu wrote: Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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/ ___ 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/ -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)7958 511 353 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
Here's another interested! On Apr 27, 2012, at 8:45 PM, Ann Black-Ziegelbein wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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/ /* Davide Cittaro, PhD Head of Bioinformatics Core Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute Via Olgettina 58 20132 Milano Italy Office: +39 02 26439140 Mail: cittaro.dav...@hsr.itmailto:cittaro.dav...@hsr.it Skype: daweonline */ http://www.5xmille.org/[cid:firma3e79.jpg]http://www.sanraffaele.org Disclaimer added by CodeTwo Exchange Rules 2007 www.codetwo.comhttp://www.codetwo.com inline: firma3e79.jpg___ 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] Interested in speaking with other institutions deploying Galaxy locally?
We are interested too. Thanks Ann for taking the initiative. -- Shantanu On Apr 27, 2012, at 3:38 PM, Anne Pajon wrote: I'm interested too. On 27 Apr 2012, at 21:13, Ann Black-Ziegelbein wrote: Thanks everyone! Glad to find some common interest. I will see if I can arrange an initial call. Hi Tyler - I was hoping we could just do a voice conference call. It would be great to meet those face to face at the Galaxy Conference in Chicago if some are attending. Thanks! Ann On 4/27/2012 3:07 PM, JIE CHEN wrote: Cool idea. I am very interested in it. One question: how could we attend the conference since we all at different place? Cheers, Tyler On Fri, Apr 27, 2012 at 12:33 PM, Mohammad Heydarian mheyd...@jhmi.edu wrote: Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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/ ___ 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/ -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)7958 511 353 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ 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/
