[galaxy-user] Secure file upload gateway for Galaxy
Hi, Our team at the University of Oslo is building a Life Science Portal based on Galaxy. We operate several standalone instances and we have the necessary sysadmin experience, but we really need to implement a more secure file upload mechanism than FTP (we do not like to send cleartext password credentials in the open ), and we understand that Galaxy does not integrate an upload method other than FTP with reference to this screencast: http://screencast.g2.bx.psu.edu/quickie_17_ftp_upload/flow.html One possible solution for this is to setup an SFTP upload server with a huge scratch space, that runs the SFTP upload gateway on one end and an IP restricted FTP server on the other, so that users can then upload/index the SFTP uploaded data into their Galaxy session via the URL upload field. This two step process might be a bit cumbersome for some of our users and we are looking for ways to simplify it. Do you have best recipes for SFTP/Aspera upload gateway integration to Galaxy? We would welcome advise on that matter. GM Best regards, -- -- George Magklaras PhD RHCE no: 805008309135525 Head of IT/Senior Systems Engineer Biotechnology Center of Oslo and the Norwegian Center for Molecular Medicine/ Vitenskapelig Databehandling (VD) - Research Computing Services - USIT EMBnet TMPC Chair http://folk.uio.no/georgios http://www.uio.no/english/services/it/research/hpc/abel/ Tel: +47 22840535 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Stitch MAF blocks
Hi, I don't undestand how to use the tool Stitch MAF blocks. I update a small bed file and now I need to run this tool, I don't understand the next step. I'm searching for Novel Linc in some RNA-seq data and I found the lncRscan tool (http://code.google.com/p/lncrscan/wiki/example) and now I have to use Stitch MAF blocks. The point is: I update the bed file, I select Fetch Alignments - Stitch MAF blocks, and then I can do nothing, I can only choose among locally cached alignments and alignments in your history. But MAF type/MAF file remain empty, in any case. Can someone be so gentle to solve my problem? Do I need to download a MAF file? Is it normally on Galaxy server, but now it is down? How can I produce a MAF file selecting only some species (29 mammals)? Thank you really much. Jennifer ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Secure file upload gateway for Galaxy
On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras georg...@biotek.uio.no wrote: Hi, Do you have best recipes for SFTP/Aspera upload gateway integration to Galaxy? We would welcome advise on that matter. Hi, I haven't implemented yet, but I'm planning on using plain scp(windows user can use WinSCP). I shouldn't have problems doing so by using this option in universe_wsgi.ini: # Add an option to the library upload form which allows authorized # non-administrators to upload a directory of files. The configured directory # must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or # sub-directories of files contained in their directory. user_library_import_dir = /local/opt/galaxy/import_dir Hope it helps, Carlos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Metagenomic filtering
Jing et al Thank you for the offer to write some code to help advance the metagenomics arena. It is certainly needed. So the problem is well known with megablast and shotgun metagenomics and without proper understanding and correct software will yield very misleading and in many cases incorrect data. For those of us who wish NOT to move to a protein level of comparison for specific reasons, we are stuck. *The Problem:* If I megablast 50 million sequences from a HiSeq run, millions of rRNA sequences will have a 99% match to all microbes rRNA genbank deposits. Not surprizing since the rRNA is highly conserved. The difference between E.coli and Shigella is 1 to 2 bases for the full 1540 bp 16s. So 16s is not useful for Genus level, and certainly not Species *So what happens:* The returned matches will have many hits to whatever model organism is in Genbank. For example E coli has 13000 entries for rRNA and Sphearotilus has 3 entries for rRNA. If the blasted sequence matches both, the results will mislead the investigator to think they have 13000 hits to E coli, EVEN if the microbe is Sphearotilus. *The cure?:* If there was a way to filter/ remove all hits ? Let say, for example, that a result has a first match (say E. coli) at 99% a second match (say Pseudomanas) at 99% and a third , forth and fifth match 99 for three other organisms. This sequence _must_ be discarded because it is a conserve sequence. Basically conserved sequence is the enemy and invalidates the entire result. * **Another problem:* If you have a reference sample with 19 non-model microbes, and you run that by HiSeq Shotgun for metagenomics and then megablast, what do you think you get? If E coli is not in the reference sample, how many hits do you think you get? Yes, 10,000 of thousands. So without removing conserved sequences, your data is wrong and you are much better served by culturing and running a Biolog metabolic panel and comparing to the sequence result. So where do we start? I have some shotgun metagenomics data from the reference sample which included the 19 microbes. That was data from a MiSeq. Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core University of Vermont Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2557 On 9/20/2013 9:17 PM, Jing Yu wrote: Hi Scott, I can do some perl programming, such as local/remote blasting. Can you specify your problem a little bit clearer, so that maybe I can write a program to do just that? Regards, Jing Gerald 16s is basically useless for identification to genus. Since I started sequencing 16s in 1992, I have come to realize that without sequencing the full 1540 bases, it is generally misleading, and even than, it is not accurate enough to nail genus on more than 1/2 the cases. However, what is your feeling on ITS and gyrase, They seem to be far more discriminating but those databases have been decommissioned sometime ago. The desirable thing would be that Galaxy or NCBI add a filter conserved genes [ ie any hit with a second choice greater than 3% distance]. Something such as that. If you (or others) are aware of such a thing, I'd love the here about it. Sincerely Scott ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Need your helps about Galaxy
Dear Dannon, I built a new cloud Galaxy instance today. Would you please tell me how to transfer given accounts from an old Galaxy to this new one? This is old Galaxy: http://galaxylocal.genenetwork.org:8080/ This is new Galaxy: http://galaxyclass.genenetwork.org/ Thanks a lot. Lei Yan Center for Integrative and Translational Genomics UTHSC ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Stitch MAF blocks
Hello, Yes, this tool functions on MAF input. For examples through several cases with this tool group, including this tool, please see: Making whole genome alignments usable for biologists publication supplemental. https://main.g2.bx.psu.edu/u/dan/p/maf Using Galaxy publication supplemental. Protocol #5 https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 The public Main server is experiencing some performance issues right now, so please give it some time before trying out the exercises your analysis. Reviewing the pages should be fine. Screencasts can be watched on any browser except Firefox (use Chrome, Safari) Thanks, Jen Galaxy team On 9/24/13 5:59 AM, Jennifer Di Tommaso wrote: Hi, I don't undestand how to use the tool Stitch MAF blocks. I update a small bed file and now I need to run this tool, I don't understand the next step. I'm searching for Novel Linc in some RNA-seq data and I found the lncRscan tool (http://code.google.com/p/lncrscan/wiki/example) and now I have to use Stitch MAF blocks. The point is: I update the bed file, I select Fetch Alignments - Stitch MAF blocks, and then I can do nothing, I can only choose among locally cached alignments and alignments in your history. But MAF type/MAF file remain empty, in any case. Can someone be so gentle to solve my problem? Do I need to download a MAF file? Is it normally on Galaxy server, but now it is down? How can I produce a MAF file selecting only some species (29 mammals)? Thank you really much. Jennifer ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Need your helps about Galaxy
As I said before, there is no easy way to do this. You just need to dump the old database and load into the new database. I would suggest making a copy of the old database with a current version of Galaxy. The migration scripts will then bring it up to date so you will have identical schemas. You should then be able to dump and load easily enough, you will just need to move the dump file between servers. -- James Taylor, Associate Professor, Biology/CS, Emory University On Mon, Sep 23, 2013 at 3:36 PM, Lei Yan leiyan2...@gmail.com wrote: Dear Dannon, I built a new cloud Galaxy instance today. Would you please tell me how to transfer given accounts from an old Galaxy to this new one? This is old Galaxy: http://galaxylocal.genenetwork.org:8080/ This is new Galaxy: http://galaxyclass.genenetwork.org/ Thanks a lot. Lei Yan Center for Integrative and Translational Genomics UTHSC ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Secure file upload gateway for Galaxy
Galaxy's FTP support uses ProFTPD, which has modules for both TLS (FTPS) and SFTP. -- James Taylor, Associate Professor, Biology/CS, Emory University On Tue, Sep 24, 2013 at 7:58 AM, Georgios Magklaras georg...@biotek.uio.no wrote: Hi, Our team at the University of Oslo is building a Life Science Portal based on Galaxy. We operate several standalone instances and we have the necessary sysadmin experience, but we really need to implement a more secure file upload mechanism than FTP (we do not like to send cleartext password credentials in the open ), and we understand that Galaxy does not integrate an upload method other than FTP with reference to this screencast: http://screencast.g2.bx.psu.edu/quickie_17_ftp_upload/flow.html One possible solution for this is to setup an SFTP upload server with a huge scratch space, that runs the SFTP upload gateway on one end and an IP restricted FTP server on the other, so that users can then upload/index the SFTP uploaded data into their Galaxy session via the URL upload field. This two step process might be a bit cumbersome for some of our users and we are looking for ways to simplify it. Do you have best recipes for SFTP/Aspera upload gateway integration to Galaxy? We would welcome advise on that matter. GM Best regards, -- -- George Magklaras PhD RHCE no: 805008309135525 Head of IT/Senior Systems Engineer Biotechnology Center of Oslo and the Norwegian Center for Molecular Medicine/ Vitenskapelig Databehandling (VD) - Research Computing Services - USIT EMBnet TMPC Chair http://folk.uio.no/georgios http://www.uio.no/english/services/it/research/hpc/abel/ Tel: +47 22840535 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] your video of using cloudman
Elwood: With large fastq files your best option will be either using public server (which is having difficulties today) or running a local instance of Galaxy. We are very much aware that the public site is not behaving well. It will be back on-line today and in the coming weeks we will be switching underlying infrastructure brining much needed relief to all Galaxy users at once. The best venue for posting such questions is out galaxy-user mailing list (I CC'ed it here). Thank you and sorry for the main site troubles. anton On Tue, Sep 24, 2013 at 11:29 AM, Elwood Linney ellin...@gmail.com wrote: Hello, Because of the problems with Galaxy online, I am looking into using Galaxy on the cloud but even with all the information it sometimes is confusing for individuals who wish to use existing Galaxy in a specific manner. In your video of transferring datasets to the cloud you used URLs for relatively small files, but under normal circumstances with Galaxy online, this does not work for large files. I generally work with fastq files of about 16gb in size. Would I be able to transfer this size of file via URL to the cloud or would I have to use some other means (for galaxy online I use fetch)? Rather that bother you with this question, is there a specific address that I should send this type of question to (like the user list--though it seems like there is so much disfunctional with Galaxy online that it takes a few weeks to get a repy from that)? Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Center -- Anton Nekrutenko Associate Professor Dept. of Biochemistry and Molecular Biology www.galaxyproject.org (814) 826-3051 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Need your helps about Galaxy
Thanks, James. I worked it out by downloading my data files and workflow. For some reason MACS still doesn't work. Any ideas? Lawrence T Reiter, PhD UTHSC, Memphis, TN On Sep 24, 2013, at 11:32 AM, James Taylor ja...@jamestaylor.org wrote: As I said before, there is no easy way to do this. You just need to dump the old database and load into the new database. I would suggest making a copy of the old database with a current version of Galaxy. The migration scripts will then bring it up to date so you will have identical schemas. You should then be able to dump and load easily enough, you will just need to move the dump file between servers. -- James Taylor, Associate Professor, Biology/CS, Emory University On Mon, Sep 23, 2013 at 3:36 PM, Lei Yan leiyan2...@gmail.com wrote: Dear Dannon, I built a new cloud Galaxy instance today. Would you please tell me how to transfer given accounts from an old Galaxy to this new one? This is old Galaxy: http://galaxylocal.genenetwork.org:8080/ This is new Galaxy: http://galaxyclass.genenetwork.org/ Thanks a lot. Lei Yan Center for Integrative and Translational Genomics UTHSC ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Metagenomic filtering
Hi all - Not to derail the conversation, but I wanted to point out some Galaxy resources that may help when considering how to approach solution. These may be knowns, but thought I'd put them out there just in case. See below. Best! Jen Galaxy team There are at least three public Galaxy instances that focus heavily on Metagenomics. Maybe worth a look? http://wiki.galaxyproject.org/PublicGalaxyServers Just do a browser search on metagenomics to find on page. May be others, but these are top 3. The Tool Shed may or may not contain specialized tools from these servers. Asking to have those tools made available via TS route is can be done through direct contact. Other repos may have tools that fit or could be tuned. Tool authors own tools - changes could potentially be incorporated through direct contact. Or, as is open source, used as baseline with attribution if that doesn't work out. http://toolshed.g2.bx.psu.edu/ Making a Galaxy Trello ticket for new tools and discussing new tool development on the galaxy-...@bx.psu.edu list may help you find other Galaxy community developers working on similar projects. Tickets are not just for the Galaxy core team, and even though the issue to solve is scientific, a technical implementation seems to be where this is going (new tool or existing tool tuning). http://wiki.galaxyproject.org/Issues - Inbox is where this would go. Final home almost certainly Tool Shed (same for all tools), but possibility of also including on Galaxy Main server also exists once there are a valid repo and it is determined to be a good fit (resource, etc.). On 9/24/13 7:17 AM, Scott Tighe wrote: Jing et al Thank you for the offer to write some code to help advance the metagenomics arena. It is certainly needed. So the problem is well known with megablast and shotgun metagenomics and without proper understanding and correct software will yield very misleading and in many cases incorrect data. For those of us who wish NOT to move to a protein level of comparison for specific reasons, we are stuck. *The Problem:* If I megablast 50 million sequences from a HiSeq run, millions of rRNA sequences will have a 99% match to all microbes rRNA genbank deposits. Not surprizing since the rRNA is highly conserved. The difference between E.coli and Shigella is 1 to 2 bases for the full 1540 bp 16s. So 16s is not useful for Genus level, and certainly not Species *So what happens:* The returned matches will have many hits to whatever model organism is in Genbank. For example E coli has 13000 entries for rRNA and Sphearotilus has 3 entries for rRNA. If the blasted sequence matches both, the results will mislead the investigator to think they have 13000 hits to E coli, EVEN if the microbe is Sphearotilus. *The cure?:* If there was a way to filter/ remove all hits ? Let say, for example, that a result has a first match (say E. coli) at 99% a second match (say Pseudomanas) at 99% and a third , forth and fifth match 99 for three other organisms. This sequence _must_ be discarded because it is a conserve sequence. Basically conserved sequence is the enemy and invalidates the entire result. * **Another problem:* If you have a reference sample with 19 non-model microbes, and you run that by HiSeq Shotgun for metagenomics and then megablast, what do you think you get? If E coli is not in the reference sample, how many hits do you think you get? Yes, 10,000 of thousands. So without removing conserved sequences, your data is wrong and you are much better served by culturing and running a Biolog metabolic panel and comparing to the sequence result. So where do we start? I have some shotgun metagenomics data from the reference sample which included the 19 microbes. That was data from a MiSeq. Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core University of Vermont Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2557 On 9/20/2013 9:17 PM, Jing Yu wrote: Hi Scott, I can do some perl programming, such as local/remote blasting. Can you specify your problem a little bit clearer, so that maybe I can write a program to do just that? Regards, Jing Gerald 16s is basically useless for identification to genus. Since I started sequencing 16s in 1992, I have come to realize that without sequencing the full 1540 bases, it is generally misleading, and even than, it is not accurate enough to nail genus on more than 1/2 the cases. However, what is your feeling on ITS and gyrase, They seem to be far more discriminating but those databases have been decommissioned sometime ago. The desirable thing would be that Galaxy or NCBI add a filter conserved genes [ ie any hit with a second choice greater than 3% distance]. Something such as that. If you (or others) are aware of such a thing, I'd love the here about it. Sincerely Scott
Re: [galaxy-user] Need your helps about Galaxy
Hi Lawrence, What version of MACS are you running? The Galaxy wrapper in galaxy-dist supports v1.3. I am 99% certain that the latest Cloudman image is the same, but Dannon can correct me. The two Tool Shed repos for MACS support v1.4 and v2.0.10. Making sure that the wrapper binary are a match might be the first place to check - these can get easily confused, especially when binaries install with un-versioned symbolic links by default. If you are re-running a workflow/job that came from the public Main server, and running galaxy-dist/central, then you want to use the v1.3 binary, unless purposefully upgrading both wrapper binary. The workflow reproducibility tracking will alert you about a change in tool versions and permit you to select updated tools upon execution (once tool is configured) if from the /same exact wrapper/tool/, but not if a /different wrapper/tool/repo/ - so will likely take a workflow edit to change out the tool in this case if upgrading to newer MACS version. I noticed that the tool form README link for the MACS v2.0.10 wrapper is incorrect, copy link add an .rst to find doc. Fairly certain these are expected to be .txt - I'll ask our team if this is a Tool Shed or repo input issue if extension different. Full help for installing tools from the Tool Shed is here: http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance And current wrapper/binary versions in galaxy-dist/central are listed here: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies With help for managing those dependencies here: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Hopefully this helps, Jen Galaxy team On 9/24/13 9:41 AM, Reiter, Larry T wrote: Thanks, James. I worked it out by downloading my data files and workflow. For some reason MACS still doesn't work. Any ideas? Lawrence T Reiter, PhD UTHSC, Memphis, TN -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] History will not load?
Hi Maria, Yes, this is a known issue and we have been working on resolving it today. A red banner is up on the public Main server with a description. That said, from my own testing when you first sent this in to a test I just did now, there appears to be some improvement already. When fully cleared the banner will update. Thank you for your patience, Jen Galaxy team On 9/24/13 6:13 AM, Maria Hoffman wrote: Hello, Unfortunately, it appears as though the history will not load again this AM and the jobs I have set to run last night (cuffdiff) have not completed either. Sorry to keep bothering you guys. Maria On Mon, Sep 23, 2013 at 2:36 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello Maria, The issue has been resolved. Our apologies for the inconvenience, Jen Galaxy team On 9/22/13 11:55 AM, Maria Hoffman wrote: Hello, I have been having trouble with Galaxy since yesterday. I have been trying to run cuffdiff which has been waiting to run since Friday afternoon and now my history will not even load (red error message shows up). Any incite would be much appreciated. Maria ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.org http://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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] de novo RNA-Seq workflow
Hi Carlos, We don't have a Trinity workflow available and I've looked through all of the donated community tutorials and have not been able to find one there, either. The Tool Shed has a newer feature that permits Workflow sharing, but that also lacks a RNA-seq assembly-analysis workflow. The closest I came was this post, over a year ago to the galaxy-...@bx.psu.edu mailing list. The general path outlined seems reasonable and is similar to what you would find in the Trinity documentation: http://dev.list.galaxyproject.org/building-a-full-trinity-workflow-from-assembly-through-analysis-td4655675.html Just to let you now, Jeremy (the wrapper author) let me know that the Trinity wrapper in the Tool Shed may be slightly outdated compared to the most recent binaries, so keep this in mind if you decide to use it. Reviewing publications that make use of this tool is probably the best approach. Or you could explore NGS hubs such as seqanswers.com to find out what is available/being discussed. Sorry that we could not help out more with this specific analysis, Best, Jen Galaxy team On 9/12/13 8:50 AM, Carlos Canchaya wrote: Hi guys, I am looking for a de novo RNA-seq workflow that uses trinity. Any idea if there is one available? Bests, Carlos Carlos Canchaya ccanch...@gmail.com ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
