[galaxy-dev] Problem to download mercurial egg

Moving the question over to development list http://wiki.galaxyproject.org/MailingLists Original Message Subject:[galaxy-user] Problem to download mercurial egg Date: Fri, 24 May 2013 14:17:11 +0200 From: Marc DELOGER To: Hello, I tried to download several

Re: [galaxy-dev] Tophat problem

Hi Zain, On 5/19/13 1:35 PM, Zain A Alvi wrote: Hi Jen, Thank you for the information regarding the FastQ information. It was really helpful. Lately, I have been getting the following error: "Error getting history update from this server- Bad Gateway". This occurred after I tried to reuplo

Re: [galaxy-dev] bad gateway?

Hi Megan, This issue is now resolved on the public Main instance. Thanks for reporting the problem, Jen Galaxy team On 5/19/13 8:44 PM, Megan Wilson wrote: Hi, The main page (analyze data) keeps coming back with a message saying "error getting history updates from the server: bad gateway" a

Re: [galaxy-dev] Recall: [External] Re: [galaxy-user] Question on galaxy data visualization

OK, Glad things are working out! Jen Galaxy team On 5/16/13 11:49 AM, Sun, Wenping [USA] wrote: Sun, Wenping [USA] would like to recall the message, "[External] Re: [galaxy-user] Question on galaxy data visualization". -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxypro

Re: [galaxy-dev] Step 3 of "get Microbial Data" install

Hi Sarah, NCBI made some changes and the scripts to obtain all of this data in one go are considered deprecated (for now - a ticket to update the scripts is open here: https://trello.com/c/ehx5Gvr7). You may be able to work out how to adjust them yourself, if familiar with how the data is org

Re: [galaxy-dev] Galaxy Keeps Freezing

Hi Kim, We were able to resolve this in another thread, so am going to just close this out. Take care, Jen Galaxy team On 4/30/13 5:50 AM, Kim Spradling wrote: I have been trying to join the intervals of two datasets side-by-side using the public Main instance, but the job never finishes. I'

Re: [galaxy-dev] Galaxy Jobs Waiting to Run for Several Days

Hello, The public Main Galaxy server has been very busy this last week. Hopefully most if not all of your work has completed by now, but if not, the best strategy is to leave jobs running and not to stop/restart them. If certain work is more urgent that others, run those first. Jobs are exec

Re: [galaxy-dev] Tophat problem

Hi Zain, I believe we already worked out the .fastqsanger/grooming part of this question in another thread. But for others reading this post, this is a help link: See "FASTQ" http://wiki.galaxyproject.org/Support#Dataset_special_cases Our RNA-exercise covers and example workflow: https://main

Re: [galaxy-dev] Galaxy Keeps Freezing

Hi Kim, The main public Galaxy server is very busy right now. Also, this message usually occurs when a user is doing something at the exact moment when the server is at a certain stages during an update (we did one yesterday). Sorry if this was confusing! When you say that the job never fini

Re: [galaxy-dev] [galaxy-user] List of genomes

Hello Yongde, The list of genomes is gathered from many sources and is comprehensive to facilitate external display functionality (at UCSC - main and microbial-, Ensembl, Wormbase, etc.). When assigning a dataset in a standard format to one of these sources, those

Re: [galaxy-dev] Tophat didn't run

lease tell me how to point to the v2 binaries (how to change symbolic links) ? Thanks in advance, Sarah Jennifer Jackson a écrit : Hi Sarah, It still sounds like there is a path problem - this is why the tools are looking in the wrong loc file. When bowtie2/tophat2 installs, it will create

Re: [galaxy-dev] Tophat didn't run

nary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file. Epilog : job finished at jeu. avril 11 14:57:18 CEST 2013 Thanks in advance, Sarah Jennifer Jackson a écrit : Hi Sarah, Let's try to sort this out. Your problem does

Re: [galaxy-dev] Tophat didn't run

Hi Sarah, Let's try to sort this out. Your problem does not seem to be the same as in the question referenced, but we can see. First - just to double check - since setting up the genome, you have restarted the server? If not, do that first and check to see if that fixes the problem. Basically,

[galaxy-dev] problem with BWA

Hello Celso, This problem is occurring in a local install of Galaxy? If so, then you will need to set up the reference genome to be used with tools. Instructions to do so are on these wiki pages: Basic instructions, you will need to move on to "Advanced Configuration": http://wiki.galaxyproje

[galaxy-dev] Galaxy April 1, 2013 Distribution

Galaxy April 1, 2013 Distribution * Complete News Brief * *Highlights:* * Job running configuration changes and refactoring of job runner plugins

[galaxy-dev] Knowing who is currently logged into your system

Hi Akshay, I am going to post your question over to the galaxy-...@bx.psu.edu mailing list, to give it better viability. You could probably run an sql query against a database table to find out this information, but there may be a better way. Let's see if someone has a method worked out they

[galaxy-dev] hello Newbie questions about galaxy and clustering

Hello Jereme, I am going to post your question over to the galaxy-...@bx.psu.edu mailing list to give it better visibility to the development community. This is also where you will want to post future questions about your local install. http://wiki.galaxyproject.org/MailingLists For you ques

Re: [galaxy-dev] customtrack visualisation

Hi Shaun. Is this still an issue for you this morning, on the public Main Galaxy server at https://main.g2.bx.psu.edu/? I am unable to reproduce with a test dataset: - bed custom track - datatype = "customtrack" - database = "hg18" "display at UCSC main" is functional, and it is the only exte

Re: [galaxy-dev] Problems with Galaxy-Project since 3/14/2013 update

Hi Zain, This is in also in reply to your email this morning: 5:54 AM (US Pacific Coast Time) [galaxy-dev] Same Problems with Galaxy-Project since 3/14/2013 update For any jobs that may have been terminated, please re-run. As the servers/clusters were brought back up online following the hardwa

[galaxy-dev] Reminder: Galaxy Main & Test Server downtime for hardware relocation Thursday, March 14, 2013

Original Notice Date: Thursday, March 7, 2013 Reminder Notice Date: Friday, March 8, 2013 Greetings Galaxy Main & Test Users, The Galaxy Public Main Galaxy Server at http://main.g2.bx.psu.edu (usegalaxy.org) and Test Galaxy Server at http://te

Re: [galaxy-dev] Contributing to genome indexes on rsync server

Hi Brad (and Roman), The team has talked about this in detail. There are a few wrinkles with just pulling in indexes - Dan is doing some work that could change this later on, but for now, the rsync will continue to point to the same location as Main's genome data source. This means that there

Re: [galaxy-dev] Tools and Data

Hello Shenwiyn, For a genome such as "nt", then you will want all of the files starting with "nt" in this directory. Use the ones ending in "md5" to double check that the download was complete for each. If you are looking to just including the databases on the Public Main Galaxy server, ther

[galaxy-dev] Galaxy Main & Test Server downtime for hardware relocation Thursday, March 14, 2013

Notice Date: Thursday, March 7, 2013 Greetings Galaxy Main & Test Users, The Galaxy Public Main Galaxy Server at http://main.g2.bx.psu.edu (usegalaxy.org) and Test Galaxy Server at http://test.g2.bx.psu.edu will be down on Thursday, March 14, while the t

Re: [galaxy-dev] Problem running Tophat for Illumina

em...@gmail.com> > *Date:* 2013-02-22 01:22 > *To:* Jennifer Jackson <mailto:j...@bx.psu.edu> > *CC:* galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu> > *Subject:* Re: [galaxy-dev] Problem running Tophat for Illumina > Ok, you're right, I did ask something si

[galaxy-dev] Support Question

Hi Tomas, I am going to move your question over to the galaxy-...@bx.psu.edu mailing list, which give it better exposure to the development community. This is where you will also want to post questions about local installs going forward. Someone here may have advice about this tool - but real

Re: [galaxy-dev] Contributing to genome indexes on rsync server

Hi Brad, I really like this idea. I'm not going to open a ticket yet but talk with Dan/team about some options. We have an alternate directory structure modeled from last fall I'd like to get in place before we start something like this ( is not yet implemented, but it or something similar wo

Re: [galaxy-dev] BWA mapping taking >48 hours

Stefano, Certain jobs have up to 72 hours of run time on the public Main Galaxy server at https://main.g2.bx.psu.edu (usegalaxy.org). Other sites or your own site may have other limits. Jobs last different time lengths in general depending on processing needs and the capabilities of the serv

Re: [galaxy-dev] Problem running Tophat for Illumina

cftools:/usr/local/galaxy/installs/bin/cufflinks-2.0.2.Linux_x86_64:/usr/local/galaxy/installs/bin/express-1.2.2-linux_x86_64:/usr/local/galaxy/installs/bin/bwa-0.6.2:/usr/local/galaxy/installs/bin/fastx:/usr/local/galaxy/installs/bin/lastz-distrib-1.02.00:/usr/local/! galaxy/ins talls/bin/lastz

Re: [galaxy-dev] Problem running Tophat for Illumina

Hi Greg, The problem here and the confusion between the Bowtie loc files are likely related. Do you have both bowtie/bowtie2 and tophat/tophat2 installed? And the tool wrappers for all versions are active? I though we resolved this earlier but maybe you installed a new tool or updated? The w

Re: [galaxy-dev] where to announce transcript annotation file in local Galaxy install

Maxim, Brad is correct - to supply a reference annotation file to Cufflinks, the file must in the active history at the time the tool is executed. Then when setting the options for "Use Reference Annotation:" on the tool form, the pull-down will select from datasets in the right history panel

Re: [galaxy-dev] Error when trying to display data on gene track

Hello, The link appears to be one that is generated from this link (link to "GeneTrack"): "view in GeneTrack" Not this link (link to "UCSC Browser", same as in tutorials, and probably the one you want to be using anyway): "display at UCSC main" GeneTrack is no longer supported, although i

[galaxy-dev] Galaxy February 8, 2013 Distribution & News Brief

Galaxy Feb 8, 2013 Distribution & News Brief *Complete News Brief * *Highlights:* * /Improvements/ to our release process

Re: [galaxy-dev] Why "upload" to Local Instance rather than "import"?

Hi Greg, I believe that you do not need to actually copy the data to your workstation (although you could ...) - instead, symbolically link it from the external drive to your workstation so that it appears local. Then upload from that path. The data library upload "by path" option will follow

Re: [galaxy-dev] galaxy error

. Bassam Tork. On 2/6/13 12:13 PM, Jennifer Jackson wrote: Hi Bassam, First, I am going to post your question to the galaxy-...@bx.psu.edu mailing list. This is where local and cloud install Galaxy questions can get the best exposure to the development community. Next, this isn't neces

[galaxy-dev] galaxy error

Hi Bassam, First, I am going to post your question to the galaxy-...@bx.psu.edu mailing list. This is where local and cloud install Galaxy questions can get the best exposure to the development community. Next, this isn't necessarily an error. And was the full line really this? nohup: ignori

Re: [galaxy-dev] installing phylop

files (per chromosome)? Thanks, -Dina On Feb 1, 2013, at 11:55 PM, Jennifer Jackson wrote: Hi Dina, These data are available from USCS in their downloads area at http://genome.ucsc.edu. See the left side bar for the 'Downloads' link, then navigate to the genome release and tra

Re: [galaxy-dev] installing phylop

Hi Dina, These data are available from USCS in their downloads area at http://genome.ucsc.edu. See the left side bar for the 'Downloads' link, then navigate to the genome release and track files (are clearly labeled). Best, Jen Galaxy team Jennifer Hillman-Jackson Galaxy Support and Trainin

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

ies wikis to have some changes as well to address the same. Thanks for comments and hope this helps! Jen Galaxy team Can you please rephrase the above so I can follow it? Thank you... -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, February 01, 2013 9:

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

there anything else I need to change at this point. Regards, -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Thursday, January 31, 2013 6:45 PM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] install reference genome Bwa and Bowti

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

Hello Hakeem, It is difficult to troubleshoot without knowing all the exact details of your configuration, but it sounds as if you are on the right path and the last few bits should be easy to reconcile with our documentation. In particular, check that the builds.txt file contains the genomes

[galaxy-dev] Galaxy January 11, 2013 Distribution & News Brief

*Galaxy January 11, 2013 Distribution & News Brief* * Complete News Brief * * Highlights:* * /*GCC2013 Training Day Topic Nomination closes TODAY!*/ Read more...

[galaxy-dev] macs error for chipseq data

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

[galaxy-dev] Galaxy December 20, 2012 Distribution & News Brief

.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 36ad8aa7b922 *Best wishes for a safe and happy holiday*, /*The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>*/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on

Re: [galaxy-dev] Extracting bacterial seq from cordinates

ed all option just coordinates; Chr1 however the out put is empty. Thanks Kanwar On Wed, Dec 19, 2012 at 10:07 AM, Jennifer Jackson <mailto:j...@bx.psu.edu>> wrote: Hello, Both datasets can be loaded and the "custom reference genome" option used with the tool &#

Re: [galaxy-dev] Extracting bacterial seq from cordinates

d other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson 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] Reference Genomes for NGS Tools - A Couple Questions

ther Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using "reply all" in your mail client. To manage yo

Re: [galaxy-dev] Data library and symbolic links

35042 Rennes cedex, France Tél: +33 (0) 2 99 84 74 17 ___ 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://l

Re: [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?

7;t work. What am I doing wrong? Thanks On Wed, Dec 12, 2012 at 9:23 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote: Hello Sachit, Instructions for setting up local indexes are in our wiki here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

[galaxy-dev] Local galaxy

the server ? Is it stored under databases ? Thanks. Selvi Ramalingam Sent from my iPhone -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using "reply all" in your mail client. To m

Re: [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?

t: http://lists.bx.psu.edu/ -- Jennifer Jackson 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/

[galaxy-dev] December 3, 2012 Distribution & News Brief

.org/GalaxyUpdates/2012_12>*/. * http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org* new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r f364d992270c * Thanks for using Galaxy!* The Gala

Re: [galaxy-dev] [galaxy-user] Stitch Gene blocks return empty result???

sing "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:

Re: [galaxy-dev] NGS assembly?

. ___ 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/ -- Jennifer Jackson http://galaxyp

[galaxy-dev] Is there any timeout in Galaxy

Hi Akshay, Please post all technical questions directly to the galaxy-dev mailing list. I'm sure we'll be able to help out shortly, Jen Galaxy team http://wiki.galaxyproject.org/Support#Mailing_Lists Hello, My name is Akshay and I am a computer science graduate student at UGA in Dr. Kissinger

[galaxy-dev] Galaxy November 14, 2012 Distribution & News Brief

xes>, and several usability enhancements for *Datasets*, *Datatypes*, *Tools*, and *Tool Shed* functions. / http://getgalaxy.org/// /http://bitbucket.org/galaxy/galaxy-dist/ /http://galaxy-dist.readthedocs.org/ new: $ hg clone http://www.bx.psu.edu/hg/galaxy galax

[galaxy-dev] Tools Always Failing?

sing "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

Re: [galaxy-dev] Error running cuffmerge

cm_output/ [Fri Oct 19 15:14:15 2012] Converting GTF files to SAM gtf_to_sam: invalid option -- F cufflinks v0.9.1 - Usage: cufflinks [options] http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org

[galaxy-dev] Galaxy October 5, 2012 Distribution & News Brief

rg/galaxy/galaxy-dist * new: * $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist * upgrade:* $ hg pull -u -r b5bda7a5c345 ** * Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team http://galaxyproject.org ___ Please ke

Re: [galaxy-dev] (no subject)

her Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to

[galaxy-dev] Galaxy download

n 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, pleas

[galaxy-dev] Galaxy September 20, 2012 Distribution & News Brief

lt;http://bitbucket.org/galaxy/galaxy-dist> *new: * $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist* upgrade:* $ hg pull -u -r da9d740fce31 ** *Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team http://galaxyproject.org __

[galaxy-dev] How to rotate Galaxy log file

cussion 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 Ja

Re: [galaxy-dev] error uploading to galaxy from InterMine

___ 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/ -- Jennifer Jackson http://galaxyp

[galaxy-dev] Cuffmerge

, cuffdiff, and cuffcompare) but not cuffmerge. Can you tell me how I would add it to the NGS:RNA Analysis group in our Galaxy installation? Thank you. Ken. -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the

[galaxy-dev] Galaxy September 7, 2012 Distribution & News Brief

laxy-dist *upgrade:* $ hg pull -u -r e6444e7a1685 * * *Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team -- http://galaxyproject.org http://usegalaxy.org ___ Please keep all replies on the list by using "reply all" i

Re: [galaxy-dev] Would like to Post to Galaxy List

his and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your s

Re: [galaxy-dev] fetch sequences

il client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using "rep

Re: [galaxy-dev] cuffdiff output

# Can anyone suggest how to get gene names instead of just numbers? Thanks suz ___ 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,

Re: [galaxy-dev] File upload via ftp: FileZilla

ts, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson 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 othe

Re: [galaxy-dev] E. grandis reference genome

e your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using "reply all" in you

Re: [galaxy-dev] [galaxy-user] Install Galaxy on Mac

and retrieve workflows from Mercurial? Thanks, Ted UCSC CBSE On Aug 10, 2012, at 1:06 PM, Jennifer Jackson wrote: Hi Diana, Galaxy itself will run on any recent MAC with the basic requirements (python, mercurial, etc.). The standard set-up isn't computationally intensive at all. What m

Re: [galaxy-dev] [galaxy-user] Install Galaxy on Mac

Bldg MAIL: 501 ASI Bldg Department of Entomology Penn State University University Park, PA, USA 16802 email: dx...@psu.edu office phone: 814-865-1022 dept. phone: 814-865-1895 -- Jennifer Jackson http://galaxyproject.org ___ Please kee

Re: [galaxy-dev] [galaxy-user] Install Galaxy on Mac

s you going! Jen Galaxy team On 8/10/12 9:59 AM, Jennifer Jackson wrote: Hi Edward, Sorry, the "https" is probably also a problem. I thought about commenting about that before, but was wasn't sure about how much help you would need exactly or if you were logged into bitbucket o

Re: [galaxy-dev] [galaxy-user] Install Galaxy on Mac

cussion 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 Jackson http://galaxyproj

Re: [galaxy-dev] [galaxy-user] Install Galaxy on Mac

g. 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 Gala

Re: [galaxy-dev] TopHat for paired end

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/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep al

Re: [galaxy-dev] Bowtie .loc file with fasta.1.ebwt

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/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by usi

[galaxy-dev] Starting a Cloud Instance

ev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using "reply a

[galaxy-dev] How to block anonymous access and disallow user registration‏

de, 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 Jackson http://galaxyproject.org __

Re: [galaxy-dev] bcftools

se use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson 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 othe

[galaxy-dev] Galaxy July 20, 2012 Distribution & News Brief

Galaxy July 20, 2012 Distribution & News Brief *Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_07_20* *Highlights: http://wiki.g2.bx.psu.edu/News/Jul202012%20Distribution%20News%20Brief* * *Freebayes *has moved from the /Galaxy distribution to the Galaxy's Main

[galaxy-dev] Attempting to use parallelism in BWA

and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using "reply all" in your mail client. To man

Re: [galaxy-dev] Cufflinks reference annotation

lease 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/ -- Jennifer Jackson http://ga

Re: [galaxy-dev] Restore Account

lists.bx.psu.edu/ -- Jennifer Jackson 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 us

Re: [galaxy-dev] Tophat and bowtie jobs failed!

lp, Avazeh ___ 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/ -- J

Re: [galaxy-dev] Job doesn't runnig

_ Amandin Talbot ___ 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/ -- Jennif

Re: [galaxy-dev] Liftover tool installation woes

) Thank you so much, SJ On Thu, Jul 5, 2012 at 4:43 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote: Hello Kwon, There are no known issues with the liftOver wrapper (tools / extract / liftOver_wrapper.py and liftOver_wrapper.xml). Three more troubleshooting ideas:

Re: [galaxy-dev] Liftover tool installation woes

the issue with Galaxy's job runner returning anything written to stderr as an error, mentioned here: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr Seems like it was an issue back in 2010. Has this been rectified? Again, thank you for your help, SJ On Wed, Jul 4, 2012

Re: [galaxy-dev] Liftover tool installation woes

ter way. Thanks in advance, SJ ___ 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] sanitizer for carriage return

pment 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 Jackson http://galaxyproject.org ___ Please keep all

Re: [galaxy-dev] BAM format question

hester.su...@epa.gov Jennifer Jackson ---06/29/2012 12:13:36 PM---Hello Susan, Are you still having problem with registration? From: Jennifer Jackson To: Susan Hester/RTP/USEPA/US@EPA Cc: galaxy-dev@lists.bx.psu.edu

Re: [galaxy-dev] (no subject)

Triangle Park, NC 27711 hester.su...@epa.gov ___ 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.

Re: [galaxy-dev] Fully Purged Histories and still 30% used

fer, Thanks for the update. I'm not 100% sure anymore. I've deleted/purged histories and datasets as far as I know. It's showing 80% usage. This is on the public instance. Says i'm using 79% and 160gb so that seems a bit more correct then before. On Tue, Jun 26, 2012 at 2

Re: [galaxy-dev] Fully Purged Histories and still 30% used

hanks, ___ 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/ -- Jennifer Jackson http://ga

Re: [galaxy-dev] Incomplete datasets when dowloaded from history

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/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by us

[galaxy-dev] May 11, 2012 Galaxy Development News Brief

grades include /strand coloring/, /interval datatype support/, and /tabix indexing/ (fast!!). * Updated *User Interface*, *Workflow-API* upgrades, and *Custom UCSC Display*. *http://getgalaxy.org* *new*: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist *upgrade*: % h

Re: [galaxy-dev] bowtie -X

ce at: http://lists.bx.psu.edu/ -- Jennifer Jackson 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

Re: [galaxy-dev] Loc file configuration question

_ 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/ -- Jennifer Jackson http://galaxyproject.org

[galaxy-dev] Cutadapt

- Original Message Subject:Cutadapt Date: Mon, 30 Apr 2012 13:49:53 -0500 From: Tilahun Abebe To: Jennifer Jackson Hi Jennifer, I want to use cutadapt to trim adapters on Galaxy main. It looks like it is not listed under the tools. Can you add cutadapt to Galaxy? Thanks for

Re: [galaxy-dev] Delete multiple datasets

lete all the created datasets (during testing or if I've used the wrong parameters etc) it is quite tedious to delete each individual dataset. It would be useful to see and delete any hidden datasets in a similar fashion. Thanks Shaun -- Jennife

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