Re: [galaxy-user] biomart plugin

2011-03-28 Thread Greg Von Kuster
Hello Andrea,

Make a copy of the ~/tools/data_source/biomart.xml for your local biomart 
install, and change the action in the following tag to point to it.

inputs action=http://www.biomart.org/biomart/martview; check_values=false 
method=get target=_top

Then add your new biomart tool wrapper to your tool_conf.xml file and start up 
your Galaxy instance.

For details about adding a new tool, see 
https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial.

Greg Von Kuster

On Mar 26, 2011, at 10:19 AM, Andrea Edwards wrote:

 Hello
 
 I have looked at the biomart plugin for Galaxy and this seems to allow access 
 to marts on the biomart central server.
 Is there anyway to use this plugin to access a biomart on my server if I 
 can't make my biomart available on the biomart central server.
 
 If not, would it be possible to achieve this with galaxy tools. I've heard of 
 galaxy tools but never made one so I don;t know what is involved.
 
 Failing that would i be able to use the biomart plugin to access my server if 
 I had a local installation of galaxy
 
 
 thanks
 ___
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Re: [galaxy-user] Convert SOLiD data

2011-03-28 Thread Ryan Golhar

Lishiyong,

You should not convert colorspace to base space prior to aligning reads. 
 The reason for this is that if there is an error in one of the color 
calls, it will effect all the downstream color calls.


Instead, you should use an aligner that will do the assembly in 
color-space instead.  I know there are a few out there, but don't know 
them off the top of my head.


Ryan

On 3/27/11 11:35 PM, lishiyong wrote:

Hello!

I convert SOLiD csfasta- and qual-files to fastq-files ,I want to use
the fastq-files to do denovo with *SOAPdenovo*.because the SOLiD de novo
accessory tools Require large memory .But ,I find that there're some
question for the converting .

for example:

T0202322110210103200200203001123212113333311200 ——
AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTTTTCCGAA
But I think it should to be
TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC Who knows the reason
about this.
2011-03-28

lishiyong



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Re: [galaxy-user] Sort index SAM-files automatically

2011-03-28 Thread Ryan Golhar

Jo,

Use the SAM Tools SAM-TO-BAM tool in Galaxy to convert your SAM file to 
a BAM file.


Ryan


On 3/25/11 10:35 AM, Jochen Seggewiß wrote:

Hi!

Thank you for your reply.

So that means, I should convert the csfasta  qual to fastq, map it with
Bowtie, get an SAM, convert it to BAM and then index that BAM?
How can I index BAM using GALAXY?
I haven´t found a way to get a BAM directly from GALAXY using csfasta 
qual as input files.

Best regards

Jo

Am 3/25/2011 3:13 PM, schrieb Jim Robinson:

Hi Jo,

To short-circuit confusion I'll jump in here.  I'm the developer of
IGV and igvtools,  the sorting and indexing for SAM files was added
long ago, even before indexed BAM files were possible from Java
programs.   The recommendation now is to convert to BAM and index
that,  although SAM files still work.   If the galaxy community would
like the SAM option I'm happy to have igvtools wrapped as a module,
and will help with that.

BTW,  I also have some code (xml) to wrap IGV itself as a Galaxy
visualizer,  contributed to me by a user.  As I don't have a private
Galaxy installation I'm unable to test it myself, but can make it
available if anyone is interested.

Jim



Hello!

I convert SOLiD csfasta- and qual-files to fastq-files and map those
against Hg19 (Bowtie).
I would like to use the resulting sam-files in the IGV browser (Broad
Institute).
Therefore, the sam-file need to be sorted an indexed. This could be
done using the “igvtools”.
However, it would be nicer if this sorting and indexing could be done
automatically using GALAXY.
I guess that it is certainly possible – but I do not know how.
Could anybody let me know how it works and what function I have to
use, respectively?
How can I sort the sam-file the correct way?

Thank you in advance.

Best regards

Jo
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Re: [galaxy-user] Convert SOLiD data

2011-03-28 Thread Sher, Falak
Hello collegues,
I have two questions which I could not get answered.
I have Illumina single end sequences files, and want to use  them for ChIP-Seq 
analysis.
My first question is:
In Galaxy screencasts (ChIP-Seq analysis for TAF1-protein...) he does not tell 
how he has generated the txt. format of the file used for demonstration of 
ChIP-Seq analysis.
I would like to know how I can generate that file from my Illumina sequence 
files to proceed with analysis.
My second question is,
2) How can I convert SAM/BAM formated files (generated by Bowtei mapping tool 
at Galaxy) to Wiggle or Bigwig formats.
I would be thankful for the answers and comments.
Falak



From: galaxy-user-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson 
[j...@bx.psu.edu]
Sent: Monday, March 28, 2011 9:57 AM
To: lishiyong
Cc: galaxy-user
Subject: Re: [galaxy-user] Convert SOLiD data

Hello Lishiyong,

Just to confirm, the conversion was performed at Galaxy main using NGS:
QC and manipulation - Convert SOLiD output to fastq? With the option
double encode = yes? If so, the output appears to be correct.

quote from tool help:

Double encode? - converts color calls (0123.) to pseudo-nucleotides
(ACGTN). Not necessary for bowtie. Required for BWA.

Please let us know if we can help more,

Best,

Jen
Galaxy team

On 3/27/11 8:35 PM, lishiyong wrote:
 Hello!

 I convert SOLiD csfasta- and qual-files to fastq-files ,I want to use
 the fastq-files to do denovo with *SOAPdenovo*.because the SOLiD de novo
 accessory tools Require large memory .But ,I find that there're some
 question for the converting .

 for example:

 T0202322110210103200200203001123212113333311200 ——
 AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTTTTCCGAA
 But I think it should to be
 TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC Who knows the reason
 about this.
 2011-03-28
 
 lishiyong



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http://galaxyproject.org
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Re: [galaxy-user] galaxy-user Digest, Vol 57, Issue 26

2011-03-28 Thread Jennifer Jackson

closed

On 3/28/11 7:38 AM, Brian Lam wrote:



galaxy-user-requ...@lists.bx.psu.edu wrote:


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Today's Topics:

   1. Convert SOLiD data (lishiyong)
   2. Re: biomart plugin (Greg Von Kuster)
   3. Re: Convert SOLiD data (Ryan Golhar)
   4. Re: Convert SOLiD data (Jennifer Jackson)
   5. Re: Sort  index SAM-files automatically (Ryan Golhar)


--

Message: 1
Date: Mon, 28 Mar 2011 11:35:15 +0800
From: lishiyonglishiy...@genomics.org.cn
To: galaxy-usergalaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Convert SOLiD data
Message-ID:201103281135102031...@genomics.org.cn
Content-Type: text/plain; charset=us-ascii

Hello!
   I convert SOLiD csfasta- and qual-files to fastq-files ,I want  to use 
the fastq-files to do denovo with SOAPdenovo.because the SOLiD de novo 
accessory tools Require large memory .But ,I find that there're some question 
for the converting .
for example:
T0202322110210103200200203001123212113333311200 ��  
AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTTTTCCGAA

But I think it should to be TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC  
Who knows the reason about this.
2011-03-28



lishiyong
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Message: 2
Date: Mon, 28 Mar 2011 08:57:49 -0400
From: Greg Von Kusterg...@bx.psu.edu
To: Andrea Edwardsedwar...@cs.man.ac.uk
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] biomart plugin
Message-ID:a3348bc1-7c00-4b8a-9313-de8444f44...@bx.psu.edu
Content-Type: text/plain; charset=us-ascii

Hello Andrea,

Make a copy of the ~/tools/data_source/biomart.xml for your local biomart 
install, and change the action in the following tag to point to it.

inputs action=http://www.biomart.org/biomart/martview; check_values=false method=get 
target=_top

Then add your new biomart tool wrapper to your tool_conf.xml file and start up 
your Galaxy instance.

For details about adding a new tool, see 
https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial.

Greg Von Kuster

On Mar 26, 2011, at 10:19 AM, Andrea Edwards wrote:


Hello

I have looked at the biomart plugin for Galaxy and this seems to allow access 
to marts on the biomart central server.
Is there anyway to use this plugin to access a biomart on my server if I can't 
make my biomart available on the biomart central server.

If not, would it be possible to achieve this with galaxy tools. I've heard of 
galaxy tools but never made one so I don;t know what is involved.

Failing that would i be able to use the biomart plugin to access my server if I 
had a local installation of galaxy


thanks
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Message: 3
Date: Mon, 28 Mar 2011 09:53:56 -0400
From: Ryan Golhargolha...@umdnj.edu
To: lishiyonglishiy...@genomics.org.cn
Cc: galaxy-usergalaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Convert SOLiD data
Message-ID:4d9092f4.9040...@umdnj.edu
Content-Type: text/plain; charset=windows-1252; Format=flowed

Lishiyong,

You should not convert

Re: [galaxy-user] Problems using aaChanges tool

2011-03-28 Thread Jennifer Jackson

Hi Evan,

The update to include zebrafish (and a few other genomes) should roll 
out to Galaxy main in the next few days, if not sooner. Feel free to 
check back Friday for an update if you do not see it there by then.


Thank you for your patience!

Best,

Jen
Galaxy team

On 3/28/11 8:01 AM, Evan Schwab wrote:

Hi Jen,

The aaChanges tool is still not supporting the zebrafish Zv9 build.  Can
you please fix this so that I am able to use the aaChanges tool.  It's
very important.

Thanks

Evan



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Re: [galaxy-user] server error trying to DL data from galaxy on cloud

2011-03-28 Thread karlerhard

Hello,

I'm trying to download the library files I processed on my galaxy cloud
instance, but I'm getting an error.  At the top (on the right panel) it
says Server Error and then lists the URL where the data should be and
then lists:

Module paste.exceptions.errormiddleware:143 in __call__
  try:
__traceback_supplement__ = Supplement, self, environ
app_iter = self.application(environ, start_response)
return self.make_catching_iter(app_iter, environ)
except:  app_iter = self.application(environ, start_response)
Module paste.debug.prints:98 in __call__
  try:
status, headers, body = wsgilib.intercept_output(
environ, self.app)
if status is None:
# Some error occurred  environ, self.app)
Module paste.wsgilib:544 in intercept_output
  try:
for item in app_iter:
output.write(item)
finally:
if hasattr(app_iter, 'close'):  output.write(item)
MemoryError: out of memory



Is there some easy fix to this?  I'd really like to get that data off of
the cloud instance and be able to terminate it.

thanks,

karl

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Re: [galaxy-user] A genbank to gtf converter

2011-03-28 Thread David Matthews
Hi Jen,

Many thanks for the reply. Sadly my programming is not up to anything like a 
gbk to gtf converter! The main reason I want one is that as a virologist this 
would be very useful since many viruses do not have a gtf file but do have 
genbank submissions. I know of a site that has some viruses listed together 
with GFF files but alas I cannot find a GFF to GTF converter - nightmare!!

I'll keep looking for one and if I find it I'll let you know.

Cheers
David


On 23 Mar 2011, at 18:02, Jennifer Jackson wrote:

 Hello David,
 
 This is a great idea that the team has been considering adding, but nothing 
 immediate is planned. There are some external teams that are working on 
 outside development, and this is on their list, to.
 
 If interested in what that project is doing, please see this thread:
 http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004692.html
 
 For now, if the data resides in a track at UCSC (many are, especially for 
 vertebrate genomes and it is updated daily), using the Table browser can 
 allow you to export the data in GTF and push to Galaxy with the Get Data 
 tool. Since some of the data can be large, using BX Main (our local UCSC 
 mirror) may be the best source.
 
 To do this, navigate to the target genome and track (RefSeq under Gene 
 Predictions, others under Mrna  EST), and choose output format GTF - gene 
 transfer format. Please note that the gene_id attribute in the 9th field 
 will not be populated with the gene name (will be same as transcript_id). 
 This is just how UCSC does it right now (on their list to get the full GTF 
 output set up in the TB, as far as we know). But, to get that info now, go 
 back in and reexport the same table data again as all fields from selected 
 table into Galaxy and the gene name will be in the data field named name2. 
 The text manipulation tools can help to format the data.
 
 A workflow would be a good option once you have the tool path worked out, so 
 that it can be reused without having to do it all again, for future similar 
 genbank datasets. You may even want to publish the workflow for others to 
 use, as it is very popular request, maybe add published page to explain how 
 to use/prep data for input.
 
 Apologies for the current inconvenience, but hopefully this can get you going 
 until a more direct method is implemented directly in Galaxy main.
 
 Great idea that many other users are also very interested in. Any 
 contributions (page, workflow) would be most welcomed. A tool that does the 
 extraction directly from Genbank would also be welcomed in the Tool Shed, if 
 you want to contribute.
 http://community.g2.bx.psu.edu/
 
 Best,
 
 Jen
 Galaxy team
 
 
 On 3/14/11 1:15 PM, David Matthews wrote:
 Hi again,
 
 Does anyone know of a genbank to gtf converter? I have heard such things 
 exist but never found one...
 
 Cheers
 David
 
 
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 -- 
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 http://galaxyproject.org


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Re: [galaxy-user] server error trying to DL data from galaxy on cloud

2011-03-28 Thread Enis Afgan
Hi Karl,
Hmm, not having Galaxy accessible is definitely not a step in the right
direction.
Being signed into command line is not an issue; something else must have
gone wrong. To start, please take a look at the (bottom of) galaxy log file
(and email the relevant part if you don't see how to fix it immediately);
the file is saved as /mnt/galaxyTools/galaxy-central/paster.log

As far as the location of the files in data libraries, they should be stored
in the same location as history datasets, namely
/mnt/galaxyData/files/000/dataset_ID.dat
Because all of the datasets are named simply based on the database ID, it
won't necessarily be obvious which file to get without doing some (python)
coding or doing some guess work. If you know how large your files is, you
can easily narrow your choices down by listing the contents of the given
directory and sorting it by size (using command ls -lS), then pulling out
the file(s) that you want. If several files are of approx. the same size,
open them up and see which one you want.

Good luck and let us know if you have any more trouble,
Enis


On Mon, Mar 28, 2011 at 3:35 PM, karlerh...@berkeley.edu wrote:


 Hello Enis,

 Thanks for the quick response and suggestions.  I actually did have a job
 running while I tried to download a file the first time, that's the first
 time it gave the error message.  But the jobs have long since finished and
 it's still giving the error message.

 I've been able to edit the universe_wsgi.ini file to debug = False, but
 now I'm getting an Internal server error when I try to reload the galaxy
 instance.  Should I be signed out at the command-line to reload galaxy
 from a browser?  Forgive my simplicity, I'm really not at all command-line
 savvy.

 Also, another extremely basic problem I have is I just don't know where
 the data library that holds my files is located.  Any help would be
 greatly appreciated.

 best,

 karl


  Hi Karl,
  As you see from the error message, you seem to be getting this error
  because
  the machine is running out of memory. This can in part be caused by a
  configuration option that might be set in Galaxy's universe_wsgi.ini file
  (see below).
  Did you have any jobs running while trying to download the file? Waiting
  until those finish might free up some memory.
 
  A thing to try is to connect to the instance, edit Galaxy's
  universe_wsgi.ini file to se debug = False, restart Galaxy and try
  again. Are you familiar with that at all?
  The basic steps are as follows:
  [local]$ ssh -i path to your AWS private key file ubuntu@instance
  public
  IP
  [ec2]$ sudo su galaxy
  [ec2]$ cd /mnt/galaxyTools/galaxy-central
  [ec2]$ vi universe_wsgi.ini  -- edit file (around line 226) to set: debug
  =
  False
  [ec2]$ sh run.sh --stop-daemon
  [ec2]$ sh run.sh --daemon
 
  Yet another option is to connect the instance in the same way, look
  through
  the data library on the file system and manually copy the file out of the
  instance. You can use the following command to copy the file to your
 local
  instance:
  [local]$ scp -i path to your AWS private key file ubuntu@instance
  public
  IP:/mnt/galaxyData/files/000/dataset_ID.dat .
 
  Let us know if none of this works,
  Enis
 
 
  On Mon, Mar 28, 2011 at 12:02 PM, karlerh...@berkeley.edu wrote:
 
 
  Hello,
 
  I'm trying to download the library files I processed on my galaxy cloud
  instance, but I'm getting an error.  At the top (on the right panel) it
  says Server Error and then lists the URL where the data should be and
  then lists:
 
  Module paste.exceptions.errormiddleware:143 in __call__
try:
 __traceback_supplement__ = Supplement, self, environ
 app_iter = self.application(environ, start_response)
 return self.make_catching_iter(app_iter, environ)
 except:  app_iter = self.application(environ,
  start_response)
  Module paste.debug.prints:98 in __call__
try:
 status, headers, body = wsgilib.intercept_output(
 environ, self.app)
 if status is None:
 # Some error occurred  environ, self.app)
  Module paste.wsgilib:544 in intercept_output
try:
 for item in app_iter:
 output.write(item)
 finally:
 if hasattr(app_iter, 'close'):  output.write(item)
  MemoryError: out of memory
 
 
 
  Is there some easy fix to this?  I'd really like to get that data off of
  the cloud instance and be able to terminate it.
 
  thanks,
 
  karl
 
  ___
  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:
 
   

Re: [galaxy-user] Pseudo Autosomal regions in Chrs X and Y

2011-03-28 Thread Hiram Clawson
Listed on the hg19 gateway page at the UCSC genome browser.

- Original Message -
From: David Matthews d.a.matth...@bristol.ac.uk
To: Jennifer Jackson j...@bx.psu.edu
Cc: galaxy-u...@bx.psu.edu
Sent: Monday, March 28, 2011 2:04:02 PM
Subject: Re: [galaxy-user] Pseudo Autosomal regions in Chrs X and Y

Hi,

Again, thanks for the feedback. I made my own female hg19 by deleting chrY from 
my copy of hg19 so thats OK. It still leaves the problem of how to analyse male 
transcriptomes since maps to PAR1 and 2 genes get reported as multimap reads 
which can end up being filtered out depending on how you analyse your 
transcriptome. If I knew with certainty where PAR1 and 2 are on chrY of hg19 I 
was planning to replace the nucleotides with N's on chrY so that they would no 
longer show up as a multimap problem - do you (or anyone else) happen to know 
the co-ordinates on hg19?

Cheers
David


On 23 Mar 2011, at 14:19, Jennifer Jackson wrote:

 Hi David,
 
 Right now we don't have anything built-in to filter out this type of 
 duplication automatically.
 
 As a potential option, did you know that we offer a Canonical Female build 
 for certain genomes? This may help with some of the duplication issues, if 
 the loss of novel Y is OK for your project.
 
 Please see:
 https://bitbucket.org/galaxy/galaxy-central/wiki/GenomeData
 
 Thanks for bringing up a good point!
 
 Best,
 Jen
 
 
 On 3/10/11 8:44 AM, David Matthews wrote:
 Hi All again,
 
 A separate point about the analysis of cufflinks data is the subject of
 the Pseudo Autosomal Regions in X and Y - this will make a mess of gene
 expression analysis in some cases especially because tophat will assign
 a read to both places which therefore makes it a multihit read (which
 you might then filter out) or it may double the true levels of reported
 expression. Anyone had experience/thoughts on this?
 
 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.matth...@bristol.ac.uk mailto:d.a.matth...@bristol.ac.uk
 
 
 
 
 
 
 
 
 ___
 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/
 
 -- 
 Jennifer Jackson
 http://usegalaxy.org
 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/
___
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/


Re: [galaxy-user] server error trying to DL data from galaxy on cloud

2011-03-28 Thread Enis Afgan
You're almost there, the command should be executed from your local machine
(home directory is fine) and it should look as follows:
scp -i path to keyfile
ubuntu@publicDNS:/mnt/galaxyData/files/000/dataset_11.dat
.
(note the 'ubuntu@' before the public DNS and a trailing dot (.) - the dot
means your current directory on your current machine, i.e., your home dir if
that's where you are executing the command from)

I apologize for the trouble in getting the this data out and hope it does
not keep you from using Galaxy Cloud in the future (we're looking into why
the browser-based data copy didn't work and should have a fix shortly for
the main app).

Enis

On Mon, Mar 28, 2011 at 6:16 PM, karlerh...@berkeley.edu wrote:


 Hi Enis

 I'm getting the following error at the bottom of the galaxy log:

 RuntimeError: Content returned before start_response called

 I have no idea how to fix this, but I'm trying to focus now on actually
 getting the files, as I don't really need this galaxy instance anymore.  I
 have been able to locate where my files are and which are the ones I want.

 I've tried the following command:

 scp -i path to keyfile
 publicDNS:/mnt/galaxyData/files/000/dataset_11.dat

 But I just get the scp usage statement coming back.  Is there something
 else I'm missing here?  I was executing this command in my home directory,
 do I need to be somewhere else?  I feel like I'm so close!!!

 Thanks so much for your help so far, I'd be lost otherwise.

 karl





  Hi Karl,
  Hmm, not having Galaxy accessible is definitely not a step in the right
  direction.
  Being signed into command line is not an issue; something else must have
  gone wrong. To start, please take a look at the (bottom of) galaxy log
  file
  (and email the relevant part if you don't see how to fix it immediately);
  the file is saved as /mnt/galaxyTools/galaxy-central/paster.log
 
  As far as the location of the files in data libraries, they should be
  stored
  in the same location as history datasets, namely
  /mnt/galaxyData/files/000/dataset_ID.dat
  Because all of the datasets are named simply based on the database ID, it
  won't necessarily be obvious which file to get without doing some
 (python)
  coding or doing some guess work. If you know how large your files is, you
  can easily narrow your choices down by listing the contents of the given
  directory and sorting it by size (using command ls -lS), then pulling out
  the file(s) that you want. If several files are of approx. the same size,
  open them up and see which one you want.
 
  Good luck and let us know if you have any more trouble,
  Enis
 
 
  On Mon, Mar 28, 2011 at 3:35 PM, karlerh...@berkeley.edu wrote:
 
 
  Hello Enis,
 
  Thanks for the quick response and suggestions.  I actually did have a
  job
  running while I tried to download a file the first time, that's the
  first
  time it gave the error message.  But the jobs have long since finished
  and
  it's still giving the error message.
 
  I've been able to edit the universe_wsgi.ini file to debug = False,
  but
  now I'm getting an Internal server error when I try to reload the
  galaxy
  instance.  Should I be signed out at the command-line to reload galaxy
  from a browser?  Forgive my simplicity, I'm really not at all
  command-line
  savvy.
 
  Also, another extremely basic problem I have is I just don't know where
  the data library that holds my files is located.  Any help would be
  greatly appreciated.
 
  best,
 
  karl
 
 
   Hi Karl,
   As you see from the error message, you seem to be getting this error
   because
   the machine is running out of memory. This can in part be caused by a
   configuration option that might be set in Galaxy's universe_wsgi.ini
  file
   (see below).
   Did you have any jobs running while trying to download the file?
  Waiting
   until those finish might free up some memory.
  
   A thing to try is to connect to the instance, edit Galaxy's
   universe_wsgi.ini file to se debug = False, restart Galaxy and try
   again. Are you familiar with that at all?
   The basic steps are as follows:
   [local]$ ssh -i path to your AWS private key file ubuntu@instance
   public
   IP
   [ec2]$ sudo su galaxy
   [ec2]$ cd /mnt/galaxyTools/galaxy-central
   [ec2]$ vi universe_wsgi.ini  -- edit file (around line 226) to set:
  debug
   =
   False
   [ec2]$ sh run.sh --stop-daemon
   [ec2]$ sh run.sh --daemon
  
   Yet another option is to connect the instance in the same way, look
   through
   the data library on the file system and manually copy the file out of
  the
   instance. You can use the following command to copy the file to your
  local
   instance:
   [local]$ scp -i path to your AWS private key file ubuntu@instance
   public
   IP:/mnt/galaxyData/files/000/dataset_ID.dat .
  
   Let us know if none of this works,
   Enis
  
  
   On Mon, Mar 28, 2011 at 12:02 PM, karlerh...@berkeley.edu wrote:
  
  
   Hello,
  
   I'm trying to download the library files I 

Re: [galaxy-user] Pseudo Autosomal regions in Chrs X and Y

2011-03-28 Thread Jennifer Jackson

Hi David,

The PAR regions are documented at UCSC on the hg19 genome gateway page 
(and for some other recent genomes). Start at the main page, click into 
Genomes, select hg19, then scroll down to credits:


http://genome.ucsc.edu/

quote:

The Y chromosome in this assembly contains two pseudoautosomal regions 
(PARs) that were taken from the corresponding regions in the X 
chromosome and are exact duplicates:


chrY:10001-2649520 and chrY:59034050-59363566
chrX:60001-2699520 and chrX:154931044-155260560

Hopefully this helps!
Jen

On 3/28/11 2:04 PM, David Matthews wrote:

Hi,

Again, thanks for the feedback. I made my own female hg19 by deleting chrY from 
my copy of hg19 so thats OK. It still leaves the problem of how to analyse male 
transcriptomes since maps to PAR1 and 2 genes get reported as multimap reads 
which can end up being filtered out depending on how you analyse your 
transcriptome. If I knew with certainty where PAR1 and 2 are on chrY of hg19 I 
was planning to replace the nucleotides with N's on chrY so that they would no 
longer show up as a multimap problem - do you (or anyone else) happen to know 
the co-ordinates on hg19?

Cheers
David


On 23 Mar 2011, at 14:19, Jennifer Jackson wrote:


Hi David,

Right now we don't have anything built-in to filter out this type of 
duplication automatically.

As a potential option, did you know that we offer a Canonical Female build 
for certain genomes? This may help with some of the duplication issues, if the loss of 
novel Y is OK for your project.

Please see:
https://bitbucket.org/galaxy/galaxy-central/wiki/GenomeData

Thanks for bringing up a good point!

Best,
Jen


On 3/10/11 8:44 AM, David Matthews wrote:

Hi All again,

A separate point about the analysis of cufflinks data is the subject of
the Pseudo Autosomal Regions in X and Y - this will make a mess of gene
expression analysis in some cases especially because tophat will assign
a read to both places which therefore makes it a multihit read (which
you might then filter out) or it may double the true levels of reported
expression. Anyone had experience/thoughts on this?

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.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk








___
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/


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org





--
Jennifer Jackson
http://usegalaxy.org
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/


Re: [galaxy-user] server error trying to DL data from galaxy on cloud

2011-03-28 Thread karlerhard

Excellent, it was the trailing dot that I was missing!

Thanks so much for the help, I will most certainly be using Galaxy again,
it's been very useful so far.

karl


 You're almost there, the command should be executed from your local
 machine
 (home directory is fine) and it should look as follows:
 scp -i path to keyfile
 ubuntu@publicDNS:/mnt/galaxyData/files/000/dataset_11.dat
 .
 (note the 'ubuntu@' before the public DNS and a trailing dot (.) - the
 dot
 means your current directory on your current machine, i.e., your home dir
 if
 that's where you are executing the command from)

 I apologize for the trouble in getting the this data out and hope it does
 not keep you from using Galaxy Cloud in the future (we're looking into why
 the browser-based data copy didn't work and should have a fix shortly for
 the main app).

 Enis

 On Mon, Mar 28, 2011 at 6:16 PM, karlerh...@berkeley.edu wrote:


 Hi Enis

 I'm getting the following error at the bottom of the galaxy log:

 RuntimeError: Content returned before start_response called

 I have no idea how to fix this, but I'm trying to focus now on actually
 getting the files, as I don't really need this galaxy instance anymore.
 I
 have been able to locate where my files are and which are the ones I
 want.

 I've tried the following command:

 scp -i path to keyfile
 publicDNS:/mnt/galaxyData/files/000/dataset_11.dat

 But I just get the scp usage statement coming back.  Is there something
 else I'm missing here?  I was executing this command in my home
 directory,
 do I need to be somewhere else?  I feel like I'm so close!!!

 Thanks so much for your help so far, I'd be lost otherwise.

 karl





  Hi Karl,
  Hmm, not having Galaxy accessible is definitely not a step in the
 right
  direction.
  Being signed into command line is not an issue; something else must
 have
  gone wrong. To start, please take a look at the (bottom of) galaxy log
  file
  (and email the relevant part if you don't see how to fix it
 immediately);
  the file is saved as /mnt/galaxyTools/galaxy-central/paster.log
 
  As far as the location of the files in data libraries, they should be
  stored
  in the same location as history datasets, namely
  /mnt/galaxyData/files/000/dataset_ID.dat
  Because all of the datasets are named simply based on the database ID,
 it
  won't necessarily be obvious which file to get without doing some
 (python)
  coding or doing some guess work. If you know how large your files is,
 you
  can easily narrow your choices down by listing the contents of the
 given
  directory and sorting it by size (using command ls -lS), then pulling
 out
  the file(s) that you want. If several files are of approx. the same
 size,
  open them up and see which one you want.
 
  Good luck and let us know if you have any more trouble,
  Enis
 
 
  On Mon, Mar 28, 2011 at 3:35 PM, karlerh...@berkeley.edu wrote:
 
 
  Hello Enis,
 
  Thanks for the quick response and suggestions.  I actually did have a
  job
  running while I tried to download a file the first time, that's the
  first
  time it gave the error message.  But the jobs have long since
 finished
  and
  it's still giving the error message.
 
  I've been able to edit the universe_wsgi.ini file to debug = False,
  but
  now I'm getting an Internal server error when I try to reload the
  galaxy
  instance.  Should I be signed out at the command-line to reload
 galaxy
  from a browser?  Forgive my simplicity, I'm really not at all
  command-line
  savvy.
 
  Also, another extremely basic problem I have is I just don't know
 where
  the data library that holds my files is located.  Any help would be
  greatly appreciated.
 
  best,
 
  karl
 
 
   Hi Karl,
   As you see from the error message, you seem to be getting this
 error
   because
   the machine is running out of memory. This can in part be caused by
 a
   configuration option that might be set in Galaxy's
 universe_wsgi.ini
  file
   (see below).
   Did you have any jobs running while trying to download the file?
  Waiting
   until those finish might free up some memory.
  
   A thing to try is to connect to the instance, edit Galaxy's
   universe_wsgi.ini file to se debug = False, restart Galaxy and try
   again. Are you familiar with that at all?
   The basic steps are as follows:
   [local]$ ssh -i path to your AWS private key file
 ubuntu@instance
   public
   IP
   [ec2]$ sudo su galaxy
   [ec2]$ cd /mnt/galaxyTools/galaxy-central
   [ec2]$ vi universe_wsgi.ini  -- edit file (around line 226) to set:
  debug
   =
   False
   [ec2]$ sh run.sh --stop-daemon
   [ec2]$ sh run.sh --daemon
  
   Yet another option is to connect the instance in the same way, look
   through
   the data library on the file system and manually copy the file out
 of
  the
   instance. You can use the following command to copy the file to
 your
  local
   instance:
   [local]$ scp -i path to your AWS private key file
 ubuntu@instance
   public