Re: [galaxy-dev] How to refresh static/welcome.html
Hi, Another way I found is to select the main frame in the galaxy window, do show only this frame in your browser and then do a forced refresh (crtl+F5), You can then go back to your normal galaxy window and the main frame will be refreshed. David From: o...@hpc.ufl.edu Date: Tue, 18 Dec 2012 12:57:56 -0500 To: margeem...@gmail.com CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How to refresh static/welcome.html On Dec 18, 2012, at 12:51 PM, greg margeem...@gmail.com wrote: Hi guys, When I make a change to welcome.html how do I get galaxy to start displaying the new version? Thanks, Greg In my experience you have to restart all web server paster processes. Cheers, Alex ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to refresh static/welcome.html
Hi again, In fact, much easier way (at least if you are using Firefox). Right click in the main frame this frame reload frame. No need to restart galaxy. David From: o...@hpc.ufl.edu Date: Tue, 18 Dec 2012 12:57:56 -0500 To: margeem...@gmail.com CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How to refresh static/welcome.html On Dec 18, 2012, at 12:51 PM, greg margeem...@gmail.com wrote: Hi guys, When I make a change to welcome.html how do I get galaxy to start displaying the new version? Thanks, Greg In my experience you have to restart all web server paster processes. Cheers, Alex ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Error in TopHat
And when I tried running tophat alone like this: tophat -r 20 test_ref reads_1.fq reads_2.fq I get this error: [2012-12-19 06:57:07] Beginning TopHat run (v2.0.7) --- [2012-12-19 06:57:07] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-12-19 06:57:07] Checking for Samtools Samtools version: 0.1.18.0 [2012-12-19 06:57:07] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (test_ref.*.bt On Wed, Dec 19, 2012 at 10:38 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: This is the error I am getting while running Tophat. What's causing this? I have the default hg19 index files. Error in tophat: [Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3) --- [Tue Dec 18 10:08:33 2012] Preparing output location ./tophat_out/ [Tue Dec 18 10:08:33 2012] Checking for Bowtie index files Error: Could not find Bowtie index files /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19.* TopHat v1.3.3 TopHat v1.3.3 tophat -p 4 /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19 /opt/galaxyprod/galaxy-dist/database/files/000/dataset_45.dat ___ 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] Extracting bacterial seq from cordinates
I have a bacterial genome from ncbi and woulld like to extract seq from the corresponding fasta file of bacterial genome. Since i have list of coordinates so would not be possible to extract one by one. Is there any interface within galxy that i can use. Thanks ___ 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
Hi Greg, At the very top of this wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup is a link to a related wiki: http://wiki.galaxyproject.org/Admin/Data%20Integration that has additional required set-up info. This page also includes information about how to rsync the indexes currently available on the public Main server. These are planned to be updated with many new genomes and indexes over the next few weeks, so check back in mid January if you do not find what you want now and do not want to build it yourself. Releasing Bowtie2 indexes (also used by Tophat2) into this area is planned to start in later Jan, pending any issues, but to build yourself, the basic guidelines for Bowtie can be followed with adjustments to use bowtie2-build and bowtie2_indices.loc. The Bowtie2 source tool documentation has the exact options and should be used along with our guidelines (this is true for all tools that require indexes). If you choose not to populate genomes as an admin, users can use most tools with a 'custom reference genome'. Please be aware that running tools this way will take more processing resources and storage disk for user's histories. The size of the genome is the primary factor to consider - some mix of built-in and custom genomes may be good solution. Also, FTP upload will almost certainly need to be enabled. Complete how-to details from a user's perspective are here: http://wiki.galaxyproject.org/Support#Custom_reference_genome Hopefully this gives you an option that will work, Jen Galaxy team On 12/18/12 9:40 AM, greg wrote: Hi all, I'm finishing up installing Galaxy on our local cluster. I'm at this step regarding setting up reference genomes: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup#Setting_Up_the_Reference_Genomes_for_NGS_Tools But it looks like a whole lot of manual work that needs to be done by a system administrator. I was kind of expecting this would be something end users would be able to do. I'm actually not sure we have the resources for a sys admin to install all of these reference genomes every time someone needs one. I guess here are my questions: Am I misunderstanding the process? Is there a different way that normal users can add reference genomes instead? Is there anything in the works that lets users easily add these? Is there a way to use NGS tools without installing reference genomes? Thanks, Greg ___ 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 ___ 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] copying files via galaxy API
Hi Everyone,
Is there a way to directly copy files from galaxy with the proper file
name? I'm currently using the galaxy API to download files via HTTP, but it
is very slow and would like to speed up the process of copying files
directly, but am having a hard time getting the proper file names.
Are there any suggestions on how to copy files directly from galaxy without
HTTP and with the proper filenames?
# Looking up files via API
$ ./display.py api_key
http://localhost:8080/api/libraries/86cf1d3beeec9f1c/contents/32ff5cf1b96c1df7
Member Information
--
ldda_id: 32ff5cf1b96c1df7
misc_blurb: 10,028,615 lines
name: H3K9me3_L3_FE_2.wig
data_type: txt
file_name: /galaxy-central/database/files/000/dataset_733.dat
uploaded_by: rp...@bu.edu
template_data: {}
genome_build: ?
model_class: LibraryDataset
misc_info: uploaded txt file
file_size: 48439126
metadata_data_lines: 10028615
message:
id: 32ff5cf1b96c1df7
date_uploaded: 2012-12-15T01:53:08.655366
metadata_dbkey: ?
# Downloading files using a URL like
http://127.0.0.1:8080/datasets/a4975bc1e68708d4/display?to_ext=txt
thanks,
Richard
___
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] copying files via galaxy API
file_name: /galaxy-central/database/files/000/dataset_733.dat This is the dataset location on the filesystem (perhaps relative . If you script is running on a machine that has access to the filesystem, you should be able to simply copy it. Best, J.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Extracting bacterial seq from cordinates
Jen, I have also shared history with you File 27 and 32 are fetching empty seq file. I think since bacterial genome is not having any Chr that may be the problem, I tried all option just coordinates; Chr1 however the out put is empty. Thanks Kanwar On Wed, Dec 19, 2012 at 10:07 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello, Both datasets can be loaded and the custom reference genome option used with the tool 'Fetch Sequences - Extract Genomic DNA. Details about custom genomes are grouped here in our: http://wiki.galaxyproject.org/Support#Custom_reference_genome To be specific, on the Extract tool form, you will use the option: Source for Genomic Data: as History, then for the new menu option Using reference file:, select the fasta dataset of your genome from your active history. If you have trouble, be sure to double check that your formats match those required by the tool (listed on tool's form). Detailed custom genome troubleshooting help is in the wiki above and file format troubleshooting help is here, including links to data specifications: http://wiki.galaxyproject.org/Support#Troubleshooting_tool_errors (start here, more help in following sections, same wiki) Best, Jen Galaxy team On 12/19/12 8:19 AM, shamsher jagat wrote: I have a bacterial genome from ncbi and woulld like to extract seq from the corresponding fasta file of bacterial genome. Since i have list of coordinates so would not be possible to extract one by one. Is there any interface within galxy that i can use. Thanks ___ 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 Jacksonhttp://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] Extracting bacterial seq from cordinates
Hello, The format is incorrect for the interval file - the chromosome field (c1, or the first field) should be the same as the identifier (the line) in the fasta file. In your case, this is: AF148805 Change what you have assigned as Chr1 to be AF148805 to make the correction. Take care, Jen Galaxy team On 12/19/12 4:19 PM, shamsher jagat wrote: Jen, I have also shared history with you File 27 and 32 are fetching empty seq file. I think since bacterial genome is not having any Chr that may be the problem, I tried all option just coordinates; Chr1 however the out put is empty. Thanks Kanwar On Wed, Dec 19, 2012 at 10:07 AM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello, Both datasets can be loaded and the custom reference genome option used with the tool 'Fetch Sequences - Extract Genomic DNA. Details about custom genomes are grouped here in our: http://wiki.galaxyproject.org/Support#Custom_reference_genome To be specific, on the Extract tool form, you will use the option: Source for Genomic Data: as History, then for the new menu option Using reference file:, select the fasta dataset of your genome from your active history. If you have trouble, be sure to double check that your formats match those required by the tool (listed on tool's form). Detailed custom genome troubleshooting help is in the wiki above and file format troubleshooting help is here, including links to data specifications: http://wiki.galaxyproject.org/Support#Troubleshooting_tool_errors (start here, more help in following sections, same wiki) Best, Jen Galaxy team On 12/19/12 8:19 AM, shamsher jagat wrote: I have a bacterial genome from ncbi and woulld like to extract seq from the corresponding fasta file of bacterial genome. Since i have list of coordinates so would not be possible to extract one by one. Is there any interface within galxy that i can use. Thanks ___ 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 -- 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] Urgent: Seems like tophat2 does not support --transcriptome-mismatches
It seems like tophat2 does not support --transcriptome-mismatches option but Galaxy is still configured to call tophat2 with this option when run with Full parameter setting option within Galaxy. Is there new wrapper with this fix? If not, how to remove this option from Galaxy so that tophat2 is not call with this option. I am assuming that this is specified somewhere in the wrapper. Thanks, Sachit ___ 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/
