Hi Hakeem,

Let me see if I can help. First, since you are running a local install, you will want to follow our distribution new briefs, posted to our wiki here, but also sent out to the mailing lists, twitter, etc.
http://wiki.galaxyproject.org/DevNewsBriefs

On 2/1/13 9:51 AM, Hakeem Almabrazi wrote:
Hi Jennifer,

Thank you again for your help.  I am totally newbie to Galaxy so my issues 
could be due to my experience with it but I am getting some progress slowly 
though.

Now, I am having totally different problem right now.  I am trying to load 
simple file using the Galaxy GUi but it keeps telling me it is working on it 
but nothing really going on.  I sent an email to the list but has not get 
anything back so far...


This has been reported a few times, and some users have already replied that the queued jobs completed. It is most likely that the remaining jobs sent in as questions are also simply queued jobs waiting to run, but this needs to be confirmed. We will reply once that is complete.

Where can I look for galaxy logs?  I am looking at the paster.log but it does 
not tell me much?  People online keeps talking about output/log but I am not 
sure where to go about that.

What kind of other log are you looking for? As an admin of your own instance you can get really detailed and look at everything that happens, build your own queries to pull out information into files from the database, etc. For example, this is the application log table:
http://wiki.galaxyproject.org/Admin/Internals/Application Logging
The complete data model and other details are under here:
http://wiki.galaxyproject.org/Admin/Internals


To answer your questions about SAM Tools:

Following the instructions at 
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I was confused at this 
part:

------------------------
Then start adding the entries for each build

     The file's path should include the first part of the index files' names 
(the base)
     So if they are named like reference_in.fasta.amb and are stored in 
/path/to/base/indices, the entry should be:
     reference_in /path/to/base/indices/reference_in.fasta
     a tab separating the two

-------------------
It talks about two columns rather than 4 columns.

Yes, I can see that a few of the loc file instructions are incorrect (old) where it comes to formatting. The correct instructions to follow are in the .loc files themselves. I am going to remove these sections entirely - having the content is two places makes it easy for it to get out of sync, as it is now. The definitive source for the format is the .loc file itself, whether from a repository or in the distribution. Thanks for pointing this out!

Also, I could not find bwa_index.loc.sample in the tool_data/ folder. Also, I had to add this entry or might be bowtie_indices.loc to too_data_table_conf.xml since it was not there by default and it was not mentioned anywhere in the instructions.


BWA was moved to the tool shed and out of the Galaxy distribution some months ago. Do you mean that the BWA repository in the Tool Shed did not have instructions it it for how to set up the installation with respect to data? This is currently true, and is something that is under current discussion/work (how to correctly and fully document each repository so that all dependencies are self-included - not only for repos generated by the Galaxy team but everyone!). The feedback that this is important is on target with what we thought was needed - we appreciate that you took the time to let us know.

"
For the SAM->BAM tool - in the UI, there will never be a list of genomes
- that is not one of the form options. This tool either interprets the
database assigned to the input dataset (option "Choose the source for
the reference list: Locally cashed") or allows the user to select a
genome custom reference genome (option same, but "History"). "

I got lost at the point where it explains how to test it as follow:
----------------
You can test your file by restarting the server and then opening SAM-to-BAM, 
Merge BAM files, or Generate pileup. Note that all rely on a file in the 
history that has a build assigned to it that is in your list of SAM Tools index 
builds. So you will need to set it (click the pencil icon to be able to change 
it) if it does not have that assigned to it already. This means that your build 
should be among the general builds available.
-----------------

I am not really sure if I followed this.  I could not see the pencil icon to 
change it.

The pencil icon is in the dataset box. This wiki explains, but just look at any dataset in your history and you will find it in the upper right corner:

http://wiki.galaxyproject.org/Learn/Managing%20Datasets#Dataset_Icons_.26_Text

Click on the pencil icon to reach a set of tabs that permit the editing of a dataset's attributes, including the assigned reference genome. For your test and the tool you mentioned, you will want a BAM file assigned to the database "hg19".

We have plans to simplify/restructure this document to better reflect how tools are now distributed (in the primary distribution vs the tool shed) and I am certainly interested in feedback about how to make this as easy as possible for everyone, especially new users, to follow. You can expect to see something newly reorganized within the month or so from us. It will probably be a set of documents, not just one. And as this is an open wiki, our community is welcome to then add in additional info/wikis as it seems appropriate or helpful. You can expect the dependencies wikis to have some changes as well to address the same.

Thanks for comments and hope this helps!

Jen
Galaxy team

Can you please rephrase the above so I can follow it?

Thank you...





-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Friday, February 01, 2013 9:32 AM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie!

Hi Hakeem,

The set up for samtools looks correct. If the problems that you had with
BWA/Bowtie were due to an error in our wiki, please send in the
suggested changes to me. We want this to be correct.

For the SAM->BAM tool - in the UI, there will never be a list of genomes
- that is not one of the form options. This tool either interprets the
database assigned to the input dataset (option "Choose the source for
the reference list: Locally cashed") or allows the user to select a
genome custom reference genome (option same, but "History").

So, to give this a test, run a dataset through it that has hg19 assigned
as the reference and examine the results.

If you are curious about custom genomes, which are used as fasta file
datasets from a user's history with tools (instead of installed
reference genomes), more is here:
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Take care,

Jen
Galaxy team


On 2/1/13 6:40 AM, Hakeem Almabrazi wrote:
Thank you Jennifer for your help.

I already resolved the issues with Bwa and Bowtie.  I was misled with some 
missing instructions but I managed to resolved them by searching online.  Now I 
am stuck at the SAM Tools.... displaying a reference genome....  :)...  I will 
give more details at what I am doing hopefully someone can help.

My reference fasta (hg10.fasta) file is located at 
(/usr/local/galaxy_data/hg19/samtools/)

I ran the following command to build the samtools index file
samtools faidx hg19.fasta
This generated the hg19.fasta.fai

Here is the content of the above path after running the samtools indexing 
command:

-rwxr-xr-x 1 galaxy galaxy hg19.fasta
-rw-rw-r-- 1 galaxy galaxy hg19.fasta.fai


For my ~tool-data/sam_fa_indices.loc file here is the info I am using to 
reference the index file:
############
Index<TAB>hg19<TAB>/usr/local/galaxy_data/hg19/samtools/hg19.fasta
###########

I restarted my server but I do not see anything when I go to 
GUI->NGS:SamTools->Sam-To-Bam->Choose the source for the reference 
list:<HISTORY>

Is there something I am missing or is there anything else I need to change at 
this point.

Regards,

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Thursday, January 31, 2013 6:45 PM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie!

Hello Hakeem,

It is difficult to troubleshoot without knowing all the exact details of
your configuration, but it sounds as if you are on the right path and
the last few bits should be easy to reconcile with our documentation.

In particular, check that the builds.txt file contains the genomes that
you are adding. Also, if you want to view or use our indexes (if we have
them available for your genome), or just want to double check your
indexes vs ours, the rsync service can be used. Both are described in
this wiki:
http://wiki.galaxyproject.org/Admin/Data%20Integration

I am not sure that I understand step #5, but there is another confusing
point here. You want the data and all tools under the primary Galaxy
directory hierarchy or have the alternate locations specified in the
universe config file. Also, it is important to not us symbolic paths in
the .loc files - use the full hard path to the indexed data.

Hopefully this helps! If you do need more feedback, please be sure to
leave the mailing list on the cc to help us track any reply,

Best,

Jen
Galaxy team

On 1/30/13 4:19 PM, Hakeem Almabrazi wrote:
Hi,

I just installed Galaxy in local Centos Vm.  I did my best to get
everything working ( I think).  I followed the instructions in this Wiki
(http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) to install
reference genomes for the tools Bwa and Bowtie.  Here is what I did in
details:

1.I installed all the software and added them to the PATH and everything
seems to be working.

2.Then I created the indices as explained.

3.I put all the indices in the same recommended directory structure and
gave all access rights to the Galaxy user which runs the Galaxy server.

4.I created the loc files (bowtie_indices.loc and
bowtie_indices_color.loc and bwa_index.loc) and populate them with the
recommended contents) and place them in ~/tool_data/ folder.

5.I copied the xml and py files from this location and put them into
~/tools/sr_mapping/....
https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping
This step was not mentioned in the instruction but I thought this might
be the cause.

6.I restarted the server.

Once I select NGS:Mapping tool and Bwa or Bowtie I do not see the
reference genome in the list.  Can someone tell me what I missed or how
to go about debugging it?

I appreciate any kind of help....



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