[galaxy-dev] August 11, 2014 Galaxy Distribution

2014-08-15 Thread Jennifer Jackson
August 11, 2014 Galaxy Distribution http://wiki.galaxyproject.org/News/2014_08_11_Galaxy_Distribution / https://www.docker.com// _Complete News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2014_08_11___ /Highlights:/// .Security alert http://tinyurl.com/nhgmbc5from July 31st,

[galaxy-dev] August 11, 2014 Galaxy Distribution

2014-08-12 Thread Jennifer Jackson
August 11, 2014 Galaxy Distribution http://wiki.galaxyproject.org/News/2014_08_11_Galaxy_Distribution / https://www.docker.com// _Complete News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2014_08_11___ /Highlights:/// .Security alert http://tinyurl.com/nhgmbc5from July 31st, upgrade

Re: [galaxy-dev] SAM/BAM To Counts dataset generation errors

2014-06-11 Thread Jennifer Jackson
Hello, This question and this Biostar post are the same question, correct? https://biostar.usegalaxy.org/p/7979/ Glad this is resolved. Next time, would be best to post to just one place. Thanks! Jen Galaxy team On 6/10/14 3:55 AM, Israel Bravo wrote: When trying SAM/BAM to Counts I get the

Re: [galaxy-dev] Join Paired-End reads (version 1.0.3)

2014-06-11 Thread Jennifer Jackson
Hello Julien, I don't know if you have had help already or not, but contacting the owners of this instance is the probably the quickest path to an answer (and possibly shared code). At this instance, under Help - Support, they have modified the link to point to the email address for their

Re: [galaxy-dev] sorting of files in data libraries

2014-06-11 Thread Jennifer Jackson
Hi Sarah, Data libraries are in an active enhancement phase. There are many changes recent, in progress, and planned that you can review in Trello. This is one of them, and the specific card is here: https://trello.com/c/0RnzM6lP For now, uploading with the name you wish to use in the UI

[galaxy-dev] June 2, 2014 Galaxy Distribution

2014-06-02 Thread Jennifer Jackson
June 2, 2014 Galaxy Distribution http://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution *News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2014_06_02**Highlights:* * Dataset Collections introduced * Changes to database build (dbkey) organization * Enhancements to Tool

Re: [galaxy-dev] Cannot access saved history nor saved datasets

2014-05-05 Thread Jennifer Jackson
Hi Joshua, If you are still having issues, you'll want to contact the folks running that specific instance for support. They'll know the state of the server. See this link, under the section User Support for their google group contact:

Re: [galaxy-dev] Portability and versionig in Galaxy

2014-05-05 Thread Jennifer Jackson
Hi Sally, I can point you to a few resources that explain what we are working on, what we plan to work on, and how the architecture is put together. All possible development directions versus what is prioritized because it fits the larger project goals will be hopefully be clearer after a

Re: [galaxy-dev] permanently deleting histories

2014-05-05 Thread Jennifer Jackson
Hi Jennifer, Active and Deleted histories can be permanently deleted using from the History pane Options - Saved Histories, then at the top of the middle panel click on Advanced Search, then click on status: all. Check the box for the histories to be discarded and then click on the button

[galaxy-dev] Uploading big data in local installation of galaxy

2014-05-05 Thread Jennifer Jackson
Hi Amit, You may have solved this already, but if not, there are (at least) two good options, with the second better if your data is already on the same computer that you have Galaxy running. A file 2G or over will never load through the browser - this same rule applies to a local and the

[galaxy-dev] Intersect multiple sorted BED files / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

2014-04-25 Thread Jennifer Jackson
Hello Sarah, This commit was made some time ago and is already in the distribution. Are you running the latest distribution? And you have uncommented the configuration line for this in your universe.wgsi.ini file? # Directory where chrom len files are kept, currently mainly used by

Re: [galaxy-dev] Intersect multiple sorted BED files / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

2014-04-25 Thread Jennifer Jackson
: bugfixes parent: 8835:c8b7dfb1e76d user:Dannon Baker dannonba...@me.com date:Wed Feb 13 13:28:47 2013 -0500 summary: Close branch bugfixes from PR#120 Jennifer Jackson a écrit : Hello Sarah, This commit was made some time ago and is already in the distribution. Are you

Re: [galaxy-dev] Intersect multiple sorted BED files / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

2014-04-25 Thread Jennifer Jackson
: bugfixes parent: 8835:c8b7dfb1e76d user:Dannon Baker dannonba...@me.com date:Wed Feb 13 13:28:47 2013 -0500 summary: Close branch bugfixes from PR#120 Jennifer Jackson a écrit : Hello Sarah, This commit was made some time ago and is already in the distribution. Are you

[galaxy-dev] Galaxy - Cloudman

2014-04-24 Thread Jennifer Jackson
Posting to the galaxy-...@bx.psu.edu mailing list. https://wiki.galaxyproject.org/MailingLists My instance of Galaxy seems to be stuck (same place since last night) and I have received the error message several times now. Pasting the error message below: *Details* user username

[galaxy-dev] Announcing the Galaxy Biostar Forum

2014-04-23 Thread Jennifer Jackson
* Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org https://biostar.usegalaxy.org/! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool

[galaxy-dev] Announcing the Galaxy Biostar Forum

2014-04-23 Thread Jennifer Jackson
Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on usegalaxy.org, a

Re: [galaxy-dev] registration problem

2014-04-22 Thread Jennifer Jackson
Hi Wesley, Carlos, We'd very much appreciate that you both took the time to report details about this issue. We captured this in the Trello ticket: https://trello.com/c/FLlynVZm This issue was closed in another thread on 2/4/2014, please see ticket for details. May a known already, but just

Re: [galaxy-dev] extract_genomic_dna.py

2014-04-08 Thread Jennifer Jackson
Hi Adhemar, Very glad this is working out for your own use. I created a ticket to include your suggested enhancement globally: https://trello.com/c/jbhy3dSM Should you wish to create a ticket in the future, this is how: https://wiki.galaxyproject.org/Issues Community contributions are

Re: [galaxy-dev] known name outputs shown in /database/files but not in galaxy windows

2014-04-03 Thread Jennifer Jackson
Hi Angelica, It appears that you are attempting to directly name the output files. Instead, use a variable naming method that permits Galaxy to actually name the files accessed by the database, using output with data tags to link any working files (with from_work_dir) and attach attributes

[galaxy-dev] Output file to history

2014-03-21 Thread Jennifer Jackson
Hi Sebastian, I'm going to move this over to the galaxy-...@bx.psu.edu mailing list so that it reaches the development community effectively. I personally do not know the answer, but I am sure we can get you some help. Best, Jen Galaxy team https://wiki.galaxyproject.org/MailingLists On

Re: [galaxy-dev] How to install bowtie2 tool in galaxy

2014-03-05 Thread Jennifer Jackson
Hi Ravi, The directory structure for the installation of ToolShed tools changed, which is why you have three directories. You perhaps had bowtie2 installed once before, then reinstalled (without completely removing the older version and associated data)? Or updated without resetting the

Re: [galaxy-dev] Reference Genome in snpEff Tool

2014-02-24 Thread Jennifer Jackson
Hi Xiaofei, It is best to keep replied on the mailing list. First, confirm that you are running the most current version of the Galaxy distribution. This should be true by default if the installation was just performed. https://wiki.galaxyproject.org/DevNewsBriefs

Re: [galaxy-dev] Unexpected behaviour when downloading HTML files

2014-02-24 Thread Jennifer Jackson
Hi Shian, I can reproduce the behavior on the public Main server (usegalaxy.org) as well. It is unintentional to my knowledge. I have opened a bug ticket to track the issue, and you can also follow it here: https://trello.com/c/Y0K7C7ay Thanks for reporting the problem! If there is more to

Re: [galaxy-dev] Unicode error manipulation of fastq

2014-02-24 Thread Jennifer Jackson
Hello Brani, I don't know if you have tried to run other tools on your file, or if you have tried this same operation on the public Main instance at http://usegalaxy.org, but my guess is that you will run into the same issue. One path is to convert the UNICODE characters to ASCII. This prior

Re: [galaxy-dev] Error in SICER tool

2014-02-20 Thread Jennifer Jackson
Hello Nikos, This is a known issue after the recent tool migrations. The ticket is here: https://trello.com/c/h9LSdfdS The root cause of the error is a missing fortran library. If you click on the eye for the associated log dataset, and scroll down through the full report down to the

Re: [galaxy-dev] Reference Genome in snpEff Tool

2014-02-17 Thread Jennifer Jackson
Hi Clint, Xiaofei, There are no current plans to include additional genomes to the SnpEff tool on the public Main Galaxy instance at http://usegalaxy.org. The best solution is to either run a local Galaxy (with sufficient resources) or what is probably easier and more practical for many

Re: [galaxy-dev] SnpEff_and_CloudMap_for_other_speices_other_than_worm (galaxy not local)

2014-02-17 Thread Jennifer Jackson
Hi Xiaofei, I just replied to the other thread about this same question, and left you on the cc. Please check out the cloud option - this is intended to be useful for those that do not want to invest in a local server or manage the associated administrative tasks. If you are working in on a

[galaxy-dev] Feb 10, 2014 Galaxy Distribution News Brief

2014-02-10 Thread Jennifer Jackson
Feb 10, 2014 Galaxy Distribution News Brief https://wiki.galaxyproject.org/News/2014_02_10_Galaxy_Distribution // *CompleteNews Brief https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10* *Highlights:* * Visualization upgrades, including Trackster CSS styling * Multiple Tools migrated

[galaxy-dev] Install tools from Toolshed

2014-01-27 Thread Jennifer Jackson
Hello Shivani, The problem is either related to 3rd party cookies being enabled or a missing configuration in the universe.wsgi.ini file. This thread, in the second part, provides the full solution:

Re: [galaxy-dev] wigToBigwig error

2014-01-15 Thread Jennifer Jackson
Hello Rui, The problems you are describing have to do with the format of the input wig dataset. It looks as if you have corrected the chromosome names to be identical to the reference genome build used (required). There are options to overcome the other issues: 1. verify that your data

Re: [galaxy-dev] wigToBigwig error

2014-01-15 Thread Jennifer Jackson
found that there are many binary/script utilities: https://github.com/adamlabadorf/ucsc_tools should I install all these by running python setup.py install or I could just copy all those executables to my own utility dir? Thanks, Rui On Wed, Jan 15, 2014 at 7:51 AM, Jennifer Jackson j

Re: [galaxy-dev] password problem

2014-01-10 Thread Jennifer Jackson
Hello Andrea, Are you still having login issues? The first thing to double check is that you confirmed your registration. Did you get an email with a link? I am wondering because the address you have below differs in capitalization from the address you are sending from, and your Galaxy

Re: [galaxy-dev] ODoSE - error when using exclusively 'external' genomes

2014-01-03 Thread Jennifer Jackson
Hello Jen, For this problem, you will need to reach the support or administrators for this public server. https://wiki.galaxyproject.org/PublicGalaxyServers#ODoSE The authors of the primary publication are probably the best contacts (I couldn't locate any others). You can find these linked

Re: [galaxy-dev] Help Needed

2014-01-03 Thread Jennifer Jackson
PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello Elsayed, Protocol help for RNA-seq analysis can be found here: https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq The QA/QC steps should be done before mapping, on individual

Re: [galaxy-dev] Help Needed

2014-01-02 Thread Jennifer Jackson
Hello Elsayed, Protocol help for RNA-seq analysis can be found here: https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq The QA/QC steps should be done before mapping, on individual datasets (such as replicates) or on partial or merged datasets as needed (if that is how

[galaxy-dev] Can REMOTE_USER be changed to another header variable?

2014-01-02 Thread Jennifer Jackson
Hello Prakash, I am going to move this over to the galaxy-...@bx.psu.edu mailing list where it will have greater visibility within our development community. Best, Jen Galaxy team https://wiki.galaxyproject.org/MailingLists#The_lists On 1/2/14 7:27

Re: [galaxy-dev] Can REMOTE_USER be changed to another header variable?

2014-01-02 Thread Jennifer Jackson
On 1/2/14 8:12 AM, Velayutham, Prakash (Prakash) wrote: Hi, I guess I would have to subscribe to that list to get status updates? Thanks, Prakash On Jan 2, 2014, at 11:09 AM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello Prakash, I am going to move this over

[galaxy-dev] Error running CCAT test

2013-12-18 Thread Jennifer Jackson
Hi Nicola, This doesn't appear to be a known functional test failure (if I am reading the logs right), but I am also not the best resource to troubleshoot this particular type of problem. I am going to move this to the dev list for more feedback. If you want to add more details about your

Re: [galaxy-dev] Trinity in local

2013-12-17 Thread Jennifer Jackson
Hello Jorge, I just replied to your other question on the galaxy-user list with all of the details about configuring tools (wrappers vs binaries). For this tool, the binary components most likely need to be installed and configured. http://trinityrnaseq.sourceforge.net Best, Jen Galaxy

Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file

2013-12-16 Thread Jennifer Jackson
Hello Javier, If you would like to see an enhancement for a tool that is sourced from the tool shed, then the repository author is the correct person to contact. Go to http://usegalaxy.org/toolshed and log in to see contact information. The repo name is bedtools. The Tool Shed also has an

Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file

2013-12-16 Thread Jennifer Jackson
. Im new with galaxy) *From:*Jennifer Jackson [mailto:j...@bx.psu.edu] *Sent:* Monday, December 16, 2013 4:03 PM *To:* Javier Simon-Sanchez; galaxy-...@bx.psu.edu *Subject:* Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file Hello Javier, If you would like to see

[galaxy-dev] inconsistent BAM-to-SAM behavior

2013-12-10 Thread Jennifer Jackson
Hi Mike, I am moving this over to the galaxy-...@bx.psu.edu mailing list as it concerns a local install. This is the best way to make contact with others working with the same type of Galaxy. https://wiki.galaxyproject.org/MailingLists A few things to provide more context that will help with

Re: [galaxy-dev] inconsistent BAM-to-SAM behavior

2013-12-10 Thread Jennifer Jackson
. I did mean the same file. I just turned off autoscaling to simplify things. I'll get back to after: unistalling package_samtools_0_118 and bam_to_sam and then just installing bam_to_sam and reviewing the how our production server is set up. Thanks Mike On 12/10/13 3:03 PM, Jennifer Jackson

Re: [galaxy-dev] ClustalW

2013-12-06 Thread Jennifer Jackson
Hi Sheri, To confirm, you are using the public Main Galaxy instance at http://usegalaxy.org? Is the dataset red (an error)? If so, would you mind submitting this as a bug report? If not red, the next best option is to share the history. If you could generate a link and email that back,

Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman

2013-11-27 Thread Jennifer Jackson
Hi Karen, HyPhy is problematic right now. Reports of failing on MAF input are the most recent on the public server, but the error you see is not outside of the scope of the problem (to my knowledge). This is the open ticket with more details: https://trello.com/c/9TMF2aJl I do not have an

Re: [galaxy-dev] Error while trying to extract DNA

2013-11-27 Thread Jennifer Jackson
Hi Alan, My guess is a format issue with the input. These are usually solved easily. Is this occurring on the public Main server at usegalaxy.org? If not, can you duplicate the problem there? Please share a link to the history (can send directly to me) with the problem if you do this and it

[galaxy-dev] how to add openstack in biocloudcentral ?

2013-11-15 Thread Jennifer Jackson
Hello Zeeshan, Let's post this over to the proper list, galaxy-...@bx.psu.edu, and see if that helps. You could also contact Brad, the git repository owner, directly about questions that involve biocloud. Best, Jen Galaxy team http://wiki.galaxyproject.org/MailingLists#The_lists On 11/15/13

[galaxy-dev] Setting a queue for torque submission

2013-11-14 Thread Jennifer Jackson
Hello, I am going to move your question over to the galaxt-...@bx.psu.edu mailing list to give it better visibility to the development/local install community. http://wiki.galaxyproject.org/MailingLists#The_lists I didn't find it over here already, but apologies if double posted. Also, since I

Re: [galaxy-dev] Converting .gff3 to 12-column .bed

2013-11-12 Thread Jennifer Jackson
was expecting the number of lines would stay the same, as they did going from .gff3 to 6-column .bed file), but I am quite inexperienced using these files. Thanking you... Lindsay On Mon, Nov 11, 2013 at 11:15 AM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello

Re: [galaxy-dev] Converting .gff3 to 12-column .bed

2013-11-11 Thread Jennifer Jackson
Hello, There are no tools directly on the public Galaxy site to transform a GFF3 dataset into a BED12 dataset. However, the Tool Shed has a repository called ' fml_gff3togtf' that includes a tool for this purpose, for use in a local install. The description is a bit bothersome in that it a

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

2013-11-08 Thread Jennifer Jackson
got the ones for bowtie1… I'm wondering what's the state in regards to this past thread and what we can do to help in here. Cheers! Roman 7 mar 2013 kl. 20:01 skrev Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu: Hi Brad (and Roman), The team has talked about this in detail

Re: [galaxy-dev] Empty bowtie2 output

2013-11-08 Thread Jennifer Jackson
Hello, The mm9 bt2 indexes were restored this morning. You can track this and other current data fixes through this Trello card: https://trello.com/c/SbizUDQt Thanks for your patience during the migration. We are moving on to data now, both corrections and updates. Jen Galaxy team On

[galaxy-dev] multiple output tool in workflow

2013-11-08 Thread Jennifer Jackson
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,

Re: [galaxy-dev] multiple output tool in workflow

2013-11-08 Thread Jennifer Jackson
/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

Re: [galaxy-dev] datacache bowtie2 for mm9 ?

2013-11-07 Thread Jennifer Jackson
).. Error: Could not find Bowtie 2 index files (/galaxy/data/mm9/mm9full/bowtie2_index/mm9full.*.bt2) *From:*Jennifer Jackson [mailto:j...@bx.psu.edu] *Sent:* Friday, September 20, 2013 4:00 PM *To:* Curtis Hendrickson (Campus) *Subject:* Re: [galaxy-dev] datacache bowtie2 for mm9 ? Thanks Curtis

Re: [galaxy-dev] Bowtie2 mm9 index

2013-11-07 Thread Jennifer Jackson
Hello Mary, The underlying data is not complete for all mm9 reference genomes for the Bowtie2/Tophat2 tools, causing the error. It is a known issue and we expect to have it corrected very soon now. We consider this important and high priority, our apologies for the confusion it caused. A

[galaxy-dev] Nov 04, 2013 Galaxy Distribution

2013-11-04 Thread Jennifer Jackson
Nov 04, 2013 Galaxy Distribution http://wiki.galaxyproject.org/News/2013_11_04_Galaxy_Distribution *usegalaxy.org* *CompleteNews Brief http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04* *Highlights:* * A/*security vulnerability*/with filter tools trapped and fixed:*Upgrade or

Re: [galaxy-dev] [galaxy-user] Inquiring

2013-10-31 Thread Jennifer Jackson
! :) Jen Galaxy team On 10/31/13 12:54 PM, Yan Luo wrote: Dear Jen, Thanks. Could you please let me know if we only need change the IP address of file universe_wsgi.ini? Then we can login by the new IP address. Is it? Best Wishes, Yan On Thu, Oct 31, 2013 at 3:45 PM, Jennifer Jackson j

[galaxy-dev] Tool XML form building bug with options from_data_table=... ?

2013-10-30 Thread Jennifer Jackson
Moving this over to galaxy-...@bx.psu.edu, the best list for tool design questions. Best! Jen, Galaxy team On 10/30/13 2:24 PM, dam...@learningpoint.ca wrote: Has anyone run into this? I'm building a general-purpose filter control on my galaxy tool xml template for enabling numeric fields to

Re: [galaxy-dev] Can not find hg_g1k_v37.fa.

2013-10-16 Thread Jennifer Jackson
Hello Shenwiyn, We can confirm that the hg_g1k_v37.fa is currently unavailable. We are working to correct this. Meanwhile, the hg_g1k_v37.2bit files is available. This can be convert to fasta using the tool twoBitToFa available from UCSC in the downloads area, under source code,

Re: [galaxy-dev] [galaxy-user] Need your helps about Galaxy

2013-10-16 Thread Jennifer Jackson
University On Wed, Oct 16, 2013 at 3:31 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Lei

Re: [galaxy-dev] Can not find hg_g1k_v37.fa.

2013-10-16 Thread Jennifer Jackson
will be adding in these notes to our rsync wiki to avoid confusion going forward. Thanks Shenwiyn, I am sure that this helped many other readers. Jen Galaxy team On 10/16/13 12:39 PM, Jennifer Jackson wrote: Hello Shenwiyn, We can confirm that the hg_g1k_v37.fa is currently unavailable. We

Re: [galaxy-dev] [galaxy-user] Need your helps about Galaxy

2013-10-16 Thread Jennifer Jackson
Lei Yan, I am very glad that this worked out! It looks like you have already helped at least one other user and I am sure others to come! We were discussing this internally while you were working. Updates to the ready-loaded data on cloud instances will be getting a make-over in the near

Re: [galaxy-dev] Consistently denied server access

2013-10-15 Thread Jennifer Jackson
Hi Rhea, Are you using the new server address? This is noted on the upload form: usegalaxy.org We will be updating the screencasts and such soon, there are other small changes that will go along with this one and we want to capture it all in one place. Meanwhile, I'll try to make this more

Re: [galaxy-dev] Solenopsis invicta genome

2013-10-11 Thread Jennifer Jackson
Hi Patrick, I think this is worth consideringand will run by team. Genomes are a bit on hold right now due to the move of the public server, but once that resumes, I have a ticket going with public requests in it. Would you please send me the details for this organism: exact accession(s),

[galaxy-dev] Trouble viewing History from a particular laptop

2013-10-10 Thread Jennifer Jackson
Hi Olivia, Our development team suggests checking the paster.log, plus, if applicable, proxy server logs. From what we know, this kind of issue generally indicate a firewall issue, but without more information, it is difficult to diagnose. Please keep replies on this mailing list instead

Re: [galaxy-dev] 2 RNAseq files in Main queue 1 week to map w/Top hat

2013-10-08 Thread Jennifer Jackson
Hi Theresa, The clusters have been on and off for most of the last few weeks. The updated server is now up and much faster! We are actively seeking feedback. If a job did end up failing due to a cluster or fileserver issue during the move, then please just re-run it. There could be many

Re: [galaxy-dev] Adding a tool to Galaxy Main Server

2013-10-07 Thread Jennifer Jackson
Hello, New tools go into the Tool Shed, links with instructions are here: http://usegalaxy.org/toolshed http://wiki.galaxyproject.org/Tool%20Shed We tweet new tool additions to let the community know about them, info and recent tweets are here:

[galaxy-dev] URL problem

2013-10-02 Thread Jennifer Jackson
Alper, Did you problem get resolved already? Maybe on the galaxy-...@bx.psu.edu mailing list? I am posting it there in case it is still open. Please reply to let us know your current status. Please drop galaxy-u...@bx.psu.edu from the to/cc on reply and future posts to this thread.

[galaxy-dev] bwa indexing not automatic?

2013-09-30 Thread Jennifer Jackson
Hi Joshua, Just to double check, you are running the latest stable distribution? There are a few different BWA wrappers in the tool shed, maybe you are using a different one than previously? Using a custom reference genome from the history with bwa is possible with the wrapper with the owner

Re: [galaxy-dev] RNAseq Map with Top Hat job in queue 4 days, 'waiting to run

2013-09-30 Thread Jennifer Jackson
Hello Theresa, Local jobs should run fairly quickly. But the NGS queue was stalled, then believed to be moving earlier (incorrectly by me), but now under review again. The grey queued jobs will eventually execute, so I wouldn't delete them quite yet.

[galaxy-dev] cleanup_datasets.py with postgresql 8.1

2013-09-26 Thread Jennifer Jackson
Posting to galaxy-...@bx.psu.edu to give the question better exposure to the development community. Please _remove the galaxy-u...@bx.psu.edu mailing list from all replies_ - we want to avoid double posts. For discussion of local Galaxy instances and the Galaxy source code, please use the

Re: [galaxy-dev] datacache bowtie2 for mm9 ?

2013-09-21 Thread Jennifer Jackson
Hello Curtis, The datacache was originally pointed to the data staging area and is now pointed to the data published area. The difference is that the published area contains data and location (.loc) files that are in synch and have completed final testing. It is your choice about whether to

Re: [galaxy-dev] Looking for brave testers. New barcode splitter outputing splitted datasets directly to the history.

2013-09-11 Thread Jennifer Jackson
Hi Carlos, Nice this is being worked on. Just wanted to mention a quick tip for loading barcode splitter output: 1- right click on the output name copy the link 2- open 'Get Data - Upload File' tool, and paste link into box. Execute. 3- Repeat for all. Data will load as dataset, no

Re: [galaxy-dev] [galaxy-user] version_command tag problem

2013-09-05 Thread Jennifer Jackson
Hi Wolfgang, I am going to re-post your question over to the galaxy-dev mailing list, which is best for local instance questions. To all: please remove the galaxy-user list from any replies. Thanks! Jen Galaxy team On 9/5/13 1:33 AM, Wolfgang Maier wrote: Hi everybody, I'm trying to add the

Re: [galaxy-dev] [galaxy-user] NoClassDefFoundError in Picard Paired Read Mate Fixer

2013-09-05 Thread Jennifer Jackson
Hello, The easiest way to ensure that dependencies are set up correctly is to install tool dependencies directly from the Tool Shed: http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_repository_dependencies:_tool_dependency You will want to use:

[galaxy-dev] about Galaxy

2013-09-04 Thread Jennifer Jackson
Hello, To use Velvet, a local, cloud, or slipstream Galaxy is needed. Then the tool can be installed from the Tool Shed and used. The screencasts Introduction to Galaxy ToolShed 1/2/3 walk through the general process when using CloudMan Galaxy: http://vimeo.com/user20484153

[galaxy-dev] URL problem

2013-08-31 Thread Jennifer Jackson
Hi Alper, There may be permissions problems if just for these two links, but I am not an expert on this. Moving post over to the galaxy-dev list, which will give it better exposure to the development team and community. You'll want to post here directly with any future local install

Re: [galaxy-dev] adding new genome to local galaxy instance

2013-08-29 Thread Jennifer Jackson
Hi Vipin, On 8/28/13 1:34 PM, Vipin TS wrote: Hello, I am slightly confused with adding a new genome to my local Galaxy instance, I am using the recent default branch 10411:c42567f43aa7 (following the documentation at http://wiki.galaxyproject.org/Admin/Data%20Integration) I have edited

Re: [galaxy-dev] No zebrafish Zv9 build

2013-08-29 Thread Jennifer Jackson
Hi Tiffany, This build is included in the public Main Galaxy instance at https://main.g2.bx.psu.edu (usegalaxy.org) and in the most current CloudMain AMI (by default). This is the full name: If you are working with a local instance, then the

Re: [galaxy-dev] how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini

2013-08-14 Thread Jennifer Jackson
Original Message Subject: Re: how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini Date: Tue, 13 Aug 2013 23:21:16 -0700 From: tin h tin6...@gmail.com To: Jennifer Jackson j...@bx.psu.edu CC: Galaxy Dev galaxy-...@bx.psu.edu Thank you

Re: [galaxy-dev] adding reference genome

2013-08-13 Thread Jennifer Jackson
Hi Vijay, For right now, using a Custom reference genome with these tools is the best solution: http://wiki.galaxyproject.org/Support#Custom_reference_genome This genome in Galaxy is sourced from UCSC, as you probably know: http://wiki.galaxyproject.org/Support#Reference_genomes The

[galaxy-dev] how to add settings of TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini

2013-08-13 Thread Jennifer Jackson
Hi Tin, I am going to move this over to the galaxy-...@bx.psu.edu mailing list (good for local install questions) to give it better viability. I am by no means the best person to help with this, so hopefully others will jump in, but just from looking at this I am wondering if you shouldn't

Re: [galaxy-dev] BWA missing index on reference genome

2013-07-26 Thread Jennifer Jackson
Hi Moritz, Pls see below On Jul 26, 2013, at 6:37 AM, Moritz Juchler juch...@stud.uni-heidelberg.de wrote: Hey, 1 I installed Galaxy locally. 2 I also have BWA installed and then used the 3 shed repository to get the bwa wrapper. 4 I have the reference genome: -rw-r--r-- 1 trr users

[galaxy-dev] Galaxy Server Questions

2013-07-15 Thread Jennifer Jackson
Hi Zain, The minimum requirements for Galaxy are pretty much any recent model computer. A basic install will load and run within a very short amount of time, following the instructions at: http://getgalaxy.org Advanced tools come from the Tool Shed. These are installed separately. No

Re: [galaxy-dev] BAM pileups bugging out

2013-06-24 Thread Jennifer Jackson
Hi Andrew, Is this on a local instance or the public Main Galaxy instance at usegalaxy.org (https://main.g2.bx.psu.edu)? Also, the exact tools being used and the order is not clear. Maybe a step is missing from what is listed? (I am just guessing) If you are using the public Main instance,

Re: [galaxy-dev] BAM pileups bugging out

2013-06-24 Thread Jennifer Jackson
: This is on the public instance. I can share my history with you right here... https://main.g2.bx.psu.edu/u/guotaek/h/galaxy-101 On Mon, Jun 24, 2013 at 6:40 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Andrew, Is this on a local instance or the public Main

Re: [galaxy-dev] [galaxy-user] How do I add Ray to Galaxy Central in the tool shed ?

2013-06-13 Thread Jennifer Jackson
Hi again, On Jun 13, 2013, at 1:23 PM, Sébastien Boisvert sebastien.boisver...@ulaval.ca wrote: Hi, On 12/06/13 05:50 PM, Jennifer Jackson wrote: Hi Sébastien, This all looks fine, except for the part about including this in the distribution. As James stated, we are moving to a model

Re: [galaxy-dev] Error in getting updates from server

2013-06-07 Thread Jennifer Jackson
Hello Mather, Queued jobs should not be deleted and restarted, but allowed to execute. The server is very busy at this time and NGS mapping jobs are among those jobs that are in the busiest queue. http://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute Just to let you know,

Re: [galaxy-dev] disk space usage

2013-06-07 Thread Jennifer Jackson
Hello Katie, When you deleted the datasets, did you also delete them permanently (purge them)? If you view the history (and all histories) under history menu's option Saved Histories, the total size will be noted, which can give you an idea about where the data in your account is located.

[galaxy-dev] June 3, 2013 Galaxy Distribution

2013-06-03 Thread Jennifer Jackson
June 3, 2013 Galaxy Distribution http://wiki.galaxyproject.org/News/2013_06_03_Galaxy_Distribution *Complete News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_03* *Highlights:* * Visualization tool updates to Scatterplot

[galaxy-dev] Problem to download mercurial egg

2013-05-24 Thread Jennifer Jackson
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 marc.delo...@igr.fr To:

Re: [galaxy-dev] populating the pull-down menu: reference genomes (built-in index)

2013-05-24 Thread Jennifer Jackson
Hello Jeannette, Data is available from our rsync server, as explained here: http://wiki.galaxyproject.org/Admin/Data%20Integration See Get the data If you need to make indexes that we do not have, each tool's original documentation will have general instructions and the Galaxy .loc file has

Re: [galaxy-dev] Problem about main.g2.bx.psu.edu is taking too long to respond.

2013-05-24 Thread Jennifer Jackson
Hi Chureerat, We emailed about this yesterday, but for others who may have noticed a few interruptions, I wanted to reply on this. There were some known, intermittent, peak usage times earlier in the week, but these should be mostly resolve. Galaxy is still busy, so if this does come up

Re: [galaxy-dev] Problem with ftp connexion to Galaxy

2013-05-24 Thread Jennifer Jackson
Hello, New accounts (created this week) cannot FTP at this time. We hope to have this resolved soon. Please feel free to contact us for an update if this is still a problem by next Friday. Our apologies for the inconvenience, Jen Galaxy team On 5/22/13 6:34 AM, Fabrice BESNARD wrote:

Re: [galaxy-dev] bad gateway?

2013-05-20 Thread Jennifer Jackson
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

Re: [galaxy-dev] Tophat problem

2013-05-20 Thread Jennifer Jackson
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

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

2013-05-16 Thread Jennifer Jackson
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

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

2013-05-08 Thread Jennifer Jackson
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

Re: [galaxy-dev] Tophat problem

2013-05-07 Thread Jennifer Jackson
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:

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