simplest way to connect RNAseq tools for a local Galaxy instance

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simplest way to connect RNAseq tools for a local Galaxy instance

Elwood Linney

I have:
1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram
2) downloaded Mac OS versions of Tophat2, Bowtie2,  and the Cufflink suite to the mac
3) have looked at the Galaxy wiki on connecting these
[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies]
4) I have gotten some useful advice from Dannon Baker on how to introduce my large datasets on the some computer into Galaxy through Admin changing some permissions

but my minimal knowledge of unix commands and tricks has me stymied

Question:
If my primary purpose is to use this local instance for the analysis of RNAseq data within my lab, what is the simplest way of connecting the programs to the Galaxy framework?

While from reviewing info on the Galaxy website I am only guessing that adding them to $PATH might be the easiest way for me to do this (but I am not exactly sure what this means or specifically how I would do it in my case).  However, I do initiate the running of Galaxy by sh run.sh on my terminal and visualizing things via my localhost port.  There is some indication from the wiki I found that this might not be good for a system initiated by sh run.sh    .

[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under "Local Jobs"

I would appreciate any specific advice on this.

Sincerely,

Elwood Linney
DUMC

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Re: simplest way to connect RNAseq tools for a local Galaxy instance

Nicholas Kline
Hi Elwood,

I am in a similar situation. Our lab is trying to connect Bowtie
version 1 to our local Galaxy framework. We are slowly making progress
with the help of people at seqanswers.com You are welcome to review
the thread I started at
http://seqanswers.com/forums/showthread.php?t=31047 since it might
contain information that relates to your situation.

If you do not receive help from this mailing list, I recommend posting
your question at seqanswers.com

Good luck!




> Message: 22
> Date: Thu, 20 Jun 2013 11:45:20 -0400
> From: Elwood Linney <[hidden email]>
> To: [hidden email]
> Subject: [galaxy-dev] simplest way to connect RNAseq tools for a local
>         Galaxy instance
> Message-ID:
>         <CAC-Zp0yDhx5Dr0ffdtRB-h=[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I have:
> 1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram
> 2) downloaded Mac OS versions of Tophat2, Bowtie2,  and the Cufflink suite
> to the mac
> 3) have looked at the Galaxy wiki on connecting these
> [http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies]
> 4) I have gotten some useful advice from Dannon Baker on how to introduce
> my large datasets on the some computer into Galaxy through Admin changing
> some permissions
>
> but my minimal knowledge of unix commands and tricks has me stymied
>
> Question:
> If my primary purpose is to use this local instance for the analysis of
> RNAseq data within my lab, what is the simplest way of connecting the
> programs to the Galaxy framework?
>
> While from reviewing info on the Galaxy website I am only guessing that
> adding them to $PATH might be the easiest way for me to do this (but I am
> not exactly sure what this means or specifically how I would do it in my
> case).  However, I do initiate the running of Galaxy by sh run.sh on my
> terminal and visualizing things via my localhost port.  There is some
> indication from the wiki I found that this might not be good for a system
> initiated by sh run.sh    .
>
> [http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under
> "Local Jobs"
>
> I would appreciate any specific advice on this.
>
> Sincerely,
>
> Elwood Linney
> DUMC
> -------------- next part --------------
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> URL: <http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20130620/9af941a9/attachment-0001.html>
>
> ------------------------------
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Re: simplest way to connect RNAseq tools for a local Galaxy instance

Jennifer Jackson
In reply to this post by Elwood Linney
Hi Elwood,

It sounds like you are getting closer, and that the instructions a few days ago from Jeremy are helping:
http://dev.list.galaxyproject.org/transferring-Trapnell-et-al-programs-into-a-one-user-instance-of-Galaxy-tc4660245.html#none

For each of these tools in #2, you will need to install them according to the instructions that comes with them from the source. However, there is one change I can mention. Symbolic links pointing from bowtie->bowtie2 and tophat->tophat2 are likely to be present in the default installation. You will want to remove those. Galaxy makes a clear distinction between the versions of the tools.

So, you have added tool's as required following the instructions in this wiki:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

And, in #3, you say that you have started to follow the instructions in this wiki:
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

Jeremy also sent you the links about how to obtain and set up the genomes and indexes.

Some of this does require limited unix-command line actions and file editing. The instructions are detailed, and some have command lines, because not all, as the exact thing to type can vary. If the line-command is entirely new, I wonder if there is someone locally with unix experience at your site that you can get help from? This last part should not take very long.

Best,
Jen
Galaxy team

On 6/20/13 8:45 AM, Elwood Linney wrote:

I have:
1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram
2) downloaded Mac OS versions of Tophat2, Bowtie2,  and the Cufflink suite to the mac
3) have looked at the Galaxy wiki on connecting these
[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies]
4) I have gotten some useful advice from Dannon Baker on how to introduce my large datasets on the some computer into Galaxy through Admin changing some permissions

but my minimal knowledge of unix commands and tricks has me stymied

Question:
If my primary purpose is to use this local instance for the analysis of RNAseq data within my lab, what is the simplest way of connecting the programs to the Galaxy framework?

While from reviewing info on the Galaxy website I am only guessing that adding them to $PATH might be the easiest way for me to do this (but I am not exactly sure what this means or specifically how I would do it in my case).  However, I do initiate the running of Galaxy by sh run.sh on my terminal and visualizing things via my localhost port.  There is some indication from the wiki I found that this might not be good for a system initiated by sh run.sh    .

[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under "Local Jobs"

I would appreciate any specific advice on this.

Sincerely,

Elwood Linney
DUMC


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
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Re: simplest way to connect RNAseq tools for a local Galaxy instance

Jeremy Goecks
Here's some specific information about what the PATH variable is for UNIX systems and how to set it: http://kb.iu.edu/data/acar.html

Many folks do the following so that you only need to add a single directory to your path:

(a) install all tools in one directory;
(b) create a "bin" directory in the tools directory;
(c) use symbolic linking ( http://kb.iu.edu/data/abbe.html ) to link tool executables into the bin directory, e.g., from the bin directory:
ln -f -s ../tophat-2.0.8/tophat tophat2
(d) add the bin directory to your path.

Good luck,
J. 


On Jun 20, 2013, at 3:34 PM, Jennifer Jackson wrote:

Hi Elwood,

It sounds like you are getting closer, and that the instructions a few days ago from Jeremy are helping:
http://dev.list.galaxyproject.org/transferring-Trapnell-et-al-programs-into-a-one-user-instance-of-Galaxy-tc4660245.html#none

For each of these tools in #2, you will need to install them according to the instructions that comes with them from the source. However, there is one change I can mention. Symbolic links pointing from bowtie->bowtie2 and tophat->tophat2 are likely to be present in the default installation. You will want to remove those. Galaxy makes a clear distinction between the versions of the tools.

So, you have added tool's as required following the instructions in this wiki:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

And, in #3, you say that you have started to follow the instructions in this wiki:
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

Jeremy also sent you the links about how to obtain and set up the genomes and indexes.

Some of this does require limited unix-command line actions and file editing. The instructions are detailed, and some have command lines, because not all, as the exact thing to type can vary. If the line-command is entirely new, I wonder if there is someone locally with unix experience at your site that you can get help from? This last part should not take very long.

Best,
Jen
Galaxy team

On 6/20/13 8:45 AM, Elwood Linney wrote:

I have:
1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram
2) downloaded Mac OS versions of Tophat2, Bowtie2,  and the Cufflink suite to the mac
3) have looked at the Galaxy wiki on connecting these
[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies]
4) I have gotten some useful advice from Dannon Baker on how to introduce my large datasets on the some computer into Galaxy through Admin changing some permissions

but my minimal knowledge of unix commands and tricks has me stymied

Question:
If my primary purpose is to use this local instance for the analysis of RNAseq data within my lab, what is the simplest way of connecting the programs to the Galaxy framework?

While from reviewing info on the Galaxy website I am only guessing that adding them to $PATH might be the easiest way for me to do this (but I am not exactly sure what this means or specifically how I would do it in my case).  However, I do initiate the running of Galaxy by sh run.sh on my terminal and visualizing things via my localhost port.  There is some indication from the wiki I found that this might not be good for a system initiated by sh run.sh    .

[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under "Local Jobs"

I would appreciate any specific advice on this.

Sincerely,

Elwood Linney
DUMC


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
Galaxy Support and Training
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/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/