mi-tools- tools_fabfile.py permissions requirements (local install)
Enis, a few things we came across: a, local install R - not the correct download url, rpy - will this be fixed? permissions: the script seems to use sudo and galaxy interchangeably, which creates an issue with permissions writing to folders. Is there a way to install as galaxy user only? If we do need the switching between sudo and galaxy - is there a set of directory permissions you suggest for the original galaxy-dist install and the galaxyToools folder? b, as a second category of questions: are there any tools that do not work on the standard cloud install? (skipped over entirely or installed but do not work?) best, joe
Note: Local install questions are normally directed to the galaxy-dev list (CC'd) rather than galaxy-user On Mon, Aug 1, 2011 at 3:21 PM, Joseph Hargitai <joseph.hargitai@einstein.yu.edu> wrote:
Enis,
a few things we came across:
a, local install
R - not the correct download url,
Which URL are you talking about? The wiki page on dependencies http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies correctly links to the R project as http://www.r-project.org/
rpy - will this be fixed?
What needs to be fixed? Moving Galaxy to rpy2? https://bitbucket.org/galaxy/galaxy-central/issue/103/upgrade-rpy-to-latest-...
permissions:
the script seems to use sudo and galaxy interchangeably, which creates an issue with permissions writing to folders.
Is there a way to install as galaxy user only?
Do you mean installing Galaxy without admin rights (i.e. without using sudo)?
If we do need the switching between sudo and galaxy - is there a set of directory permissions you suggest for the original galaxy-dist install and the galaxyToools folder?
Good question - having manually reset permissions on a test server while debugging driving mappings, I'd like to know what they should be. Are you planing on using the Linux user group functionality as part of your setup? e.g. Both your personal account and the Galaxy user account could be part of a Galaxy admin group.
b, as a second category of questions: are there any tools that do not work on the standard cloud install? (skipped over entirely or installed but do not work?)
By that do you mean of the standard tool set in the main repository? (Because there will be lots of Galaxy tools in the Tool Shed which are not in the standard cloud install). Peter
Hi Jen, I mapped illumine reads to draft genomic contigs, and try to visualize the mapping. Is there any way I can use my own reference contigs for visualization? Thanks John Xu NMSU
IGV should allow you to do this but not sure about trackbrowser in Galaxy. Vasu --- On Wed, 8/3/11, Jiannong Xu <jxu@nmsu.edu> wrote: From: Jiannong Xu <jxu@nmsu.edu> Subject: [galaxy-user] visualization To: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu> Date: Wednesday, August 3, 2011, 6:03 PM Hi Jen, I mapped illumine reads to draft genomic contigs, and try to visualize the mapping. Is there any way I can use my own reference contigs for visualization? Thanks John Xu NMSU ___________________________________________________________ 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/
Hi Assuming you know the length of your contigs, you can add them as a "custom build". Click on: 'Visualization -> 'New Track Browser' -> 'Add a Custom Build' Hope this helps. Regards, Hans On 08/04/2011 01:51 AM, vasu punj wrote:
IGV should allow you to do this but not sure about trackbrowser in Galaxy. Vasu
--- On Wed, 8/3/11, Jiannong Xu<jxu@nmsu.edu> wrote:
From: Jiannong Xu<jxu@nmsu.edu> Subject: [galaxy-user] visualization To: "galaxy-user@lists.bx.psu.edu"<galaxy-user@lists.bx.psu.edu> Date: Wednesday, August 3, 2011, 6:03 PM
Hi Jen,
I mapped illumine reads to draft genomic contigs, and try to visualize the mapping. Is there any way I can use my own reference contigs for visualization?
Thanks
John Xu NMSU
___________________________________________________________ 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:
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Jiannong, Hans is on right track. You can indeed visualize your data using Trackster, Galaxy's genome browser; Trackster is available via the Visualization tab. Here are the steps needed to visualize your dataset: (1) Use the [FASTA Manipulation --> Compute Sequence length] tool to compute lengths the contigs in your build; (2) if there are spaces in your contig names, you'll need to use only the characters before the first space as contig names because this is what the mapping tools do; use [Text Manipulation --> Convert delimiters to TAB] and then [Text Manipulation --> Cut ] to cut the first and last column from the dataset; now you should have a file in the form <contig_name><tab><contig_length> (2) Create a custom build: (a) User tab --> Custom Builds; (b) scroll to the bottom, enter a name and key for your build and copy in the contig names and lengths you created in steps (1) and (2); (3) Set the dbkey for the dataset(s) that you want to visualize by clicking on the pencil icon for each dataset and selecting your custom dbkey. (4) Use the Trackster icon next to a dataset--see attached screenshot--and insert the dataset into a new browser. Let us know if you have any problems. And, yes, we're working to make this process much easier. Best, J. On Aug 4, 2011, at 3:13 AM, Hans-Rudolf Hotz wrote:
Hi
Assuming you know the length of your contigs, you can add them as a "custom build".
Click on: 'Visualization -> 'New Track Browser' -> 'Add a Custom Build'
Hope this helps.
Regards, Hans
On 08/04/2011 01:51 AM, vasu punj wrote:
IGV should allow you to do this but not sure about trackbrowser in Galaxy. Vasu
--- On Wed, 8/3/11, Jiannong Xu<jxu@nmsu.edu> wrote:
From: Jiannong Xu<jxu@nmsu.edu> Subject: [galaxy-user] visualization To: "galaxy-user@lists.bx.psu.edu"<galaxy-user@lists.bx.psu.edu> Date: Wednesday, August 3, 2011, 6:03 PM
Hi Jen,
I mapped illumine reads to draft genomic contigs, and try to visualize the mapping. Is there any way I can use my own reference contigs for visualization?
Thanks
John Xu NMSU
___________________________________________________________ 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:
___________________________________________________________ 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:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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:
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Hi, I'm trying to get read counts or FPKM values for my miRNA NGS data on Galaxy. I have aligned the reads using Bowtie, but it appears that Cufflinks gives an error when run on the Bowtie alignments (This might have something to do with Bowtie's BAM file not being sorted). I know that Tophat alignments work well with Cufflinks, but I'm not sure if it would be possible to use Tophat for my data since miRNA don't have splice junctions. I've tried without success to parameterize Tophat to completely avoid assigning splice junctions (by setting the max intron length to 1). Is there a way I can get the Bowtie alignment to work with Cufflinks on Galaxy? Or perhaps there's a way I can parametrize Tophat as to get no splice junctions? Thanks, Mete ________________________________ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
Hi Mete, This FAQ has a workflow for sorting a Bowtie (or any) SAM file for Cufflinks: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2 Thanks! Jen Galaxy team On 8/4/11 10:27 AM, Mete Civelek wrote:
Hi,
I'm trying to get read counts or FPKM values for my miRNA NGS data on Galaxy. I have aligned the reads using Bowtie, but it appears that Cufflinks gives an error when run on the Bowtie alignments (This might have something to do with Bowtie's BAM file not being sorted). I know that Tophat alignments work well with Cufflinks, but I'm not sure if it would be possible to use Tophat for my data since miRNA don't have splice junctions. I've tried without success to parameterize Tophat to completely avoid assigning splice junctions (by setting the max intron length to 1). Is there a way I can get the Bowtie alignment to work with Cufflinks on Galaxy? Or perhaps there's a way I can parametrize Tophat as to get no splice junctions?
Thanks,
Mete
------------------------------------------------------------------------ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
___________________________________________________________ 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:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
Hi Mete, I am not sure it is the "sort" problem. I find "cufflinks" in galaxy is unstable. I have bam files from Tophat which I can run cufflinks a few days agao. But these days when I run cufflinks with these bam files, the error shows. Strangely, it can work some time. I don't know the reason. ChenYao 2011/8/9 Jennifer Jackson <jen@bx.psu.edu>
Hi Mete,
This FAQ has a workflow for sorting a Bowtie (or any) SAM file for Cufflinks: http://main.g2.bx.psu.edu/u/**jeremy/p/transcriptome-**analysis-faq#faq2<http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2>
Thanks!
Jen Galaxy team
On 8/4/11 10:27 AM, Mete Civelek wrote:
Hi,
I'm trying to get read counts or FPKM values for my miRNA NGS data on Galaxy. I have aligned the reads using Bowtie, but it appears that Cufflinks gives an error when run on the Bowtie alignments (This might have something to do with Bowtie's BAM file not being sorted). I know that Tophat alignments work well with Cufflinks, but I'm not sure if it would be possible to use Tophat for my data since miRNA don't have splice junctions. I've tried without success to parameterize Tophat to completely avoid assigning splice junctions (by setting the max intron length to 1). Is there a way I can get the Bowtie alignment to work with Cufflinks on Galaxy? Or perhaps there's a way I can parametrize Tophat as to get no splice junctions?
Thanks,
Mete
------------------------------**------------------------------** ------------ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
______________________________**_____________________________ 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:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/**Support <http://galaxyproject.org/Support> ______________________________**_____________________________ 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:
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Hi, Tophat may still be an option for you. You can filter out spliced reads by filtering column 6 (the CIGAR column) for reads that only map directly (i.e. c6=='56M' if you have a 56bp paired end read). But I agree with Jen that most likely it is a sort problem. Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews@bristol.ac.uk On 9 Aug 2011, at 07:27, yao chen wrote:
Hi Mete,
I am not sure it is the "sort" problem. I find "cufflinks" in galaxy is unstable. I have bam files from Tophat which I can run cufflinks a few days agao.
But these days when I run cufflinks with these bam files, the error shows. Strangely, it can work some time. I don't know the reason.
ChenYao
2011/8/9 Jennifer Jackson <jen@bx.psu.edu> Hi Mete,
This FAQ has a workflow for sorting a Bowtie (or any) SAM file for Cufflinks: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2
Thanks!
Jen Galaxy team
On 8/4/11 10:27 AM, Mete Civelek wrote: Hi,
I'm trying to get read counts or FPKM values for my miRNA NGS data on Galaxy. I have aligned the reads using Bowtie, but it appears that Cufflinks gives an error when run on the Bowtie alignments (This might have something to do with Bowtie's BAM file not being sorted). I know that Tophat alignments work well with Cufflinks, but I'm not sure if it would be possible to use Tophat for my data since miRNA don't have splice junctions. I've tried without success to parameterize Tophat to completely avoid assigning splice junctions (by setting the max intron length to 1). Is there a way I can get the Bowtie alignment to work with Cufflinks on Galaxy? Or perhaps there's a way I can parametrize Tophat as to get no splice junctions?
Thanks,
Mete
------------------------------------------------------------------------ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
___________________________________________________________ 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:
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-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___________________________________________________________ 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:
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I use IGV outside of Galaxy. If you download your bam and bam index files you can load those and your reference into IGV to visualise them. On 04/08/2011 00:03, Jiannong Xu wrote:
Hi Jen,
I mapped illumine reads to draft genomic contigs, and try to visualize the mapping. Is there any way I can use my own reference contigs for visualization?
Thanks
John Xu NMSU
___________________________________________________________ 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:
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participants (11)
-
David Matthews -
Hans-Rudolf Hotz -
Jennifer Jackson -
Jeremy Goecks -
Jiannong Xu -
Joseph Hargitai -
Mete Civelek -
Nicola Nadeau -
Peter Cock -
vasu punj -
yao chen