Re: [galaxy-dev] galaxy local installation
Hello Carl, The problem with the format of the website was resolved. However, I'm still wondering about the apache inquiry. Can it be done? Can I give apache the job of deploying the website instead of the run.sh script ? Furthermore, I do not want an apache proxy server, I just want apache to take care of the website Cordialement / Regards, Edgar Fernandez De : Carl Eberhard [mailto:carlfeberh...@gmail.com] Envoyé : December-12-13 5:25 PM À : fernandez Edgar Cc : Alistair Chilcott; galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy local installation Hello, Edgar - thanks for installing Galaxy! Regarding the screenshots: it looks like Galaxy's static css stylesheet isn't being loaded properly. Is this still occurring for you? Do you see anything when you try to go to http://localhost:8080/static/style/base.css in your browser? (You should see some text) Thanks, Carl On Thu, Dec 12, 2013 at 2:51 PM, fernandez Edgar edgar.fernan...@umontreal.camailto:edgar.fernan...@umontreal.ca wrote: Hello, Thank you very much for the quick answers. There were very useful. Now I hope I'm not bothering you with a couple more questions. I read more thoroughly the documentation for installing a production environment and I was wondering: 1. Is it possible to run the web server through apache but not as a proxy server? a. If so what are the steps exactly? I only found the explanation for a proxy server... 2. Will this kind of installation will work on red hat 6 enterprise server ? Cordialement / Regards, Edgar Fernandez De : Alistair Chilcott [mailto:alistair.chilc...@utas.edu.aumailto:alistair.chilc...@utas.edu.au] Envoyé : December-11-13 10:10 PM À : fernandez Edgar; galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Objet : RE: galaxy local installation Edgar, I have been exploring similar outcomes and run into similar issues. I have recently found this post http://seqanswers.com/forums/showthread.php?t=23629 That I'm sure will prove helpful to you. This show how to get it working, including the dependancies and reference genomes .. advice on securing it is already on the galaxy websites. Another observation I would make is that the vast majority of help and advice you will find on the web relates to a galaxy environments built on Ubuntu, (12.04 LTS seem to be the version of choice). The instructions above will help you install it on SUSE but I found that having to translate the steps from Ubuntu to SUSE was occasionally problematic. Hope this helps. Regards, Alistair From: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of fernandez Edgar Sent: Thursday, 12 December 2013 4:31 AM To: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: [galaxy-dev] galaxy local installation Hello, My name is Edgar Fernandez. I'm a sys. admin. at University of Montreal. I've been ask by a teacher to check out Galaxy. So I've installed locally on my computer galaxy (I'm running openSUSE x86_64 but I'll install it on SUSE Linux ia64). I've executed the run.sh script and I've somewhat successfully made the website work. I say somewhat because I have a couple of issues: 1. The website is not well displayed (refer to the attachment) 2. I've changed the value of host to 0.0.0.0 in the universe_wsgi.ini file and it still launches to 127.0.0.1 I was also wondering if there is a step by step tutorial to install all the dependencies? I'm finding myself overwhelmed with all the different dependencies. Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111tel:1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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/
Re: [galaxy-dev] galaxy local installation
Hello, Thank you very much for the quick answers. There were very useful. Now I hope I'm not bothering you with a couple more questions. I read more thoroughly the documentation for installing a production environment and I was wondering: 1. Is it possible to run the web server through apache but not as a proxy server? a. If so what are the steps exactly? I only found the explanation for a proxy server... 2. Will this kind of installation will work on red hat 6 enterprise server ? Cordialement / Regards, Edgar Fernandez De : Alistair Chilcott [mailto:alistair.chilc...@utas.edu.au] Envoyé : December-11-13 10:10 PM À : fernandez Edgar; galaxy-...@bx.psu.edu Objet : RE: galaxy local installation Edgar, I have been exploring similar outcomes and run into similar issues. I have recently found this post http://seqanswers.com/forums/showthread.php?t=23629 That I'm sure will prove helpful to you. This show how to get it working, including the dependancies and reference genomes .. advice on securing it is already on the galaxy websites. Another observation I would make is that the vast majority of help and advice you will find on the web relates to a galaxy environments built on Ubuntu, (12.04 LTS seem to be the version of choice). The instructions above will help you install it on SUSE but I found that having to translate the steps from Ubuntu to SUSE was occasionally problematic. Hope this helps. Regards, Alistair From: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of fernandez Edgar Sent: Thursday, 12 December 2013 4:31 AM To: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: [galaxy-dev] galaxy local installation Hello, My name is Edgar Fernandez. I'm a sys. admin. at University of Montreal. I've been ask by a teacher to check out Galaxy. So I've installed locally on my computer galaxy (I'm running openSUSE x86_64 but I'll install it on SUSE Linux ia64). I've executed the run.sh script and I've somewhat successfully made the website work. I say somewhat because I have a couple of issues: 1. The website is not well displayed (refer to the attachment) 2. I've changed the value of host to 0.0.0.0 in the universe_wsgi.ini file and it still launches to 127.0.0.1 I was also wondering if there is a step by step tutorial to install all the dependencies? I'm finding myself overwhelmed with all the different dependencies. Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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/
Re: [galaxy-dev] galaxy local installation
Hello, Edgar - thanks for installing Galaxy! Regarding the screenshots: it looks like Galaxy's static css stylesheet isn't being loaded properly. Is this still occurring for you? Do you see anything when you try to go to http://localhost:8080/static/style/base.css in your browser? (You should see some text) Thanks, Carl On Thu, Dec 12, 2013 at 2:51 PM, fernandez Edgar edgar.fernan...@umontreal.ca wrote: Hello, Thank you very much for the quick answers. There were very useful. Now I hope I’m not bothering you with a couple more questions. I read more thoroughly the documentation for installing a production environment and I was wondering: 1. Is it possible to run the web server through apache but not as a proxy server? a. If so what are the steps exactly? I only found the explanation for a proxy server… 2. Will this kind of installation will work on red hat 6 enterprise server ? Cordialement / Regards, Edgar Fernandez *De :* Alistair Chilcott [mailto:alistair.chilc...@utas.edu.au] *Envoyé :* December-11-13 10:10 PM *À :* fernandez Edgar; galaxy-...@bx.psu.edu *Objet :* RE: galaxy local installation Edgar, I have been exploring similar outcomes and run into similar issues. I have recently found this post http://seqanswers.com/forums/showthread.php?t=23629 That I’m sure will prove helpful to you. This show how to get it working, including the dependancies and reference genomes .. advice on securing it is already on the galaxy websites. Another observation I would make is that the vast majority of help and advice you will find on the web relates to a galaxy environments built on Ubuntu, (12.04 LTS seem to be the version of choice). The instructions above will help you install it on SUSE but I found that having to translate the steps from Ubuntu to SUSE was occasionally problematic. Hope this helps. Regards, *Alistair * *From:* galaxy-dev-boun...@lists.bx.psu.edu [ mailto:galaxy-dev-boun...@lists.bx.psu.edugalaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *fernandez Edgar *Sent:* Thursday, 12 December 2013 4:31 AM *To:* galaxy-...@bx.psu.edu *Subject:* [galaxy-dev] galaxy local installation Hello, My name is Edgar Fernandez. I’m a sys. admin. at University of Montreal. I’ve been ask by a teacher to check out Galaxy. So I’ve installed locally on my computer galaxy (I’m running openSUSE x86_64 but I’ll install it on SUSE Linux ia64). I’ve executed the run.sh script and I’ve somewhat successfully made the website work. I say somewhat because I have a couple of issues: 1. The website is not well displayed (refer to the attachment) 2. I’ve changed the value of host to 0.0.0.0 in the universe_wsgi.ini file and it still launches to 127.0.0.1 I was also wondering if there is a step by step tutorial to install all the dependencies? I’m finding myself overwhelmed with all the different dependencies. Cordialement / Regards, *Edgar Fernandez* System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication ( Bur. : *1-514-343-6111 1-514-343-6111 poste 16568* *Université de Montréal* PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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/
Re: [galaxy-dev] galaxy local installation
Edgar, I have been exploring similar outcomes and run into similar issues. I have recently found this post http://seqanswers.com/forums/showthread.php?t=23629 That I'm sure will prove helpful to you. This show how to get it working, including the dependancies and reference genomes .. advice on securing it is already on the galaxy websites. Another observation I would make is that the vast majority of help and advice you will find on the web relates to a galaxy environments built on Ubuntu, (12.04 LTS seem to be the version of choice). The instructions above will help you install it on SUSE but I found that having to translate the steps from Ubuntu to SUSE was occasionally problematic. Hope this helps. Regards, Alistair From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of fernandez Edgar Sent: Thursday, 12 December 2013 4:31 AM To: galaxy-...@bx.psu.edu Subject: [galaxy-dev] galaxy local installation Hello, My name is Edgar Fernandez. I'm a sys. admin. at University of Montreal. I've been ask by a teacher to check out Galaxy. So I've installed locally on my computer galaxy (I'm running openSUSE x86_64 but I'll install it on SUSE Linux ia64). I've executed the run.sh script and I've somewhat successfully made the website work. I say somewhat because I have a couple of issues: 1. The website is not well displayed (refer to the attachment) 2. I've changed the value of host to 0.0.0.0 in the universe_wsgi.ini file and it still launches to 127.0.0.1 I was also wondering if there is a step by step tutorial to install all the dependencies? I'm finding myself overwhelmed with all the different dependencies. Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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/
Re: [galaxy-dev] galaxy local installation
Hi Edgar please find my comments within your text below: On 12/11/2013 06:30 PM, fernandez Edgar wrote: Hello, My name is Edgar Fernandez. I’m a sys. admin. at University of Montreal. I’ve been ask by a teacher to check out Galaxy. So I’ve installed locally on my computer galaxy (I’m running openSUSE x86_64 but I’ll install it on SUSE Linux ia64). I’ve executed the run.sh script and I’ve somewhat successfully made the website work. I say somewhat because I have a couple of issues: 1.The website is not well displayed (refer to the attachment) just double checking: have you reloaded your page? 2.I’ve changed the value of host to 0.0.0.0 in the universe_wsgi.ini file and it still launches to 127.0.0.1 127.0.0.1 seems correct to me, as this is the loopback address (ie 'localhost'. I was also wondering if there is a step by step tutorial to install all the dependencies? I’m finding myself overwhelmed with all the different dependencies. well, I recommend, you first make a list of the tools you want to offer in Galaxy, and then figure out which dependencies you actually need. And then use these wiki pages: https://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies https://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies Regards, Hans-Rudolf Cordialement / Regards, ** *Edgar Fernandez* System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication ( Bur. : *1-514-343-6111 poste 16568**//* *//* */Université de Montréal/**//* PAVILLON ROGER-GAUDRY, bureau X-218 ___ 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/
[galaxy-dev] GALAXY LOCAL INSTALLATION: Remove history
Hi Galaxy devs, I've installed Galaxy in local and I see that in spite of the users remove their histories using the Delete history option, the used space is not free. As I understand reading the Galaxy documentation, after deleting the history, the history is marked as Deleted but files are not removed. After 60 days, Galaxy automatically remove them. 1. If you delete a specific history using the **Options** link at the top of the history panel, that history and all of its associated datasets will be removed from disk 60 days after you deleted the history. 2. Those specific history items ( datasets ) that you delete from one of your histories by clicking the X icon in the history item will be removed from disk after 60 days, but unless you manually delete your history, you will still be able to view the history itself ( only the dataset that you deleted from your history will be removed from disk ). I suppose this should be the default behavior too for local installations. but I did not configure anything about that and I need to confirm this is true because the used space becomes bigger each day! Is there any way to change this periodicity to less days? Thank you and regards, Rafa Hernández de Diego Genomics of Gene Expression Lab. Bioinformatics and Genomics Department Prince Felipe Research Centre (CIPF) C/ Eduardo Primo Yúfera 3 46012 Valencia, Spain ___ 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/
Re: [galaxy-dev] galaxy local installation
On Apr 8, 2013, at 5:01 PM, Yinan Wan wrote:
Hi,
I was trying to install the galaxy on my laptop and run into the following
error
Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is
almost certainly a bug in the egg distribution.
Dependency ssh requires pycrypto=2.1,!=2.4
Traceback (most recent call last):
File ./scripts/fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 345, in resolve
egg.resolve()
File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File build/bdist.linux-i686/egg/pkg_resources.py, line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (ssh 1.7.14
(/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg),
Requirement.parse('pycrypto=2.1,!=2.4'))
Fetch failed.
Because I have numpy installed which seems to be conflict to galaxy, so I was
install with virtual python environment (virtualenv), and also tried the
protection environment provided in the galaxy instruction page
(http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer),
and both came across the same error as indicated above.
Some information you may be interested:
(GalaxyENV)yinan@Macbook galaxy-dist$ python -V
Python 2.7.3
(GalaxyENV)yinan@Macbook galaxy-dist$ python scripts/get_platforms.py
macosx-10.7-x86_64-ucs2
It will be great if you can help me out.
Hi Yinan,
This is surprising, virtualenv should have resolved the conflict(s). Did you
use the --no-site-packages option when you created the env?
Also, you may be able to simply run fetch_eggs.py a second time and have it
succeed in fetching the dependency.
--nate
Thanks,
Yinan
--
Yinan Wan, graduate student
Bioinformatics and Genomics program
Huck Institutes of Life Sciences
the Pennsylvania State University
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___
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] galaxy local installation
Hi,
I was trying to install the galaxy on my laptop and run into the following
error
Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
Fetched http://eggs.galaxyproject.org/ssh/ssh-1.7.14-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is
almost certainly a bug in the egg distribution.
Dependency ssh requires pycrypto=2.1,!=2.4
Traceback (most recent call last):
File ./scripts/fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 345, in resolve
egg.resolve()
File
/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File build/bdist.linux-i686/egg/pkg_resources.py, line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (ssh 1.7.14
(/Users/yinan/Course2013Spring/IBOIS58A/galaxy-dist/eggs/ssh-1.7.14-py2.7.egg),
Requirement.parse('pycrypto=2.1,!=2.4'))
Fetch failed.
Because I have numpy installed which seems to be conflict to galaxy, so I
was install with virtual python environment (virtualenv), and also tried
the protection environment provided in the galaxy instruction page (
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer),
and both came across the same error as indicated above.
Some information you may be interested:
(GalaxyENV)yinan@Macbook galaxy-dist$ python -V
Python 2.7.3
(GalaxyENV)yinan@Macbook galaxy-dist$ python scripts/get_platforms.py
macosx-10.7-x86_64-ucs2
It will be great if you can help me out.
Thanks,
Yinan
--
Yinan Wan, graduate student
Bioinformatics and Genomics program
Huck Institutes of Life Sciences
the Pennsylvania State University
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GALAXY LOCAL INSTALLATION: Tools and Data
Hi Rafa, The .loc files in 'tool-data' directory link the index files with the actual paths so you need to configure each of the .loc files to match where the index files are placed. With that, you can put the index files anywhere you'd like on the file system (preferably outside Galaxy's home directory). As a reference for a working setup, you can rsync (portion) of the data from GalaxyMain (http://wiki.galaxyproject.org/Admin/Data%20Integration) and see how that's setup. Also, you can fire up a cloud instance and see how it's setup. Hope this helps, Enis On Thu, Feb 21, 2013 at 12:14 AM, Rafael Hernández rafah...@gmail.comwrote: Hi, I've installed Galaxy in local and following the Tool dependencieshttp://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies manual I installed all necessary tools. However for some of then such as BWA, Bowtie,... it's usually needed to create indexes. Where should I store those indexes? In the galaxy directory or in each tool directory? How can I tell galaxy where the indexes are? I find a manual's page talking about it / http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup), suggesting to organize the various index files for each build, but I don't know if these folders should be stored into Galaxy directory (eg. in tool-data directory) or what. Could you please explain this a little? Thank you and regards, Rafa Hernández de Diego Genomics of Gene Expression Lab. Bioinformatics and Genomics Department Centro de Investigación Príncipe Felipe (CIPF) C/ Eduardo Primo Yúfera 3 46012 Valencia, Spain ___ 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/
[galaxy-dev] GALAXY LOCAL INSTALLATION: Tools and Data
Hi, I've installed Galaxy in local and following the Tool dependencieshttp://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies manual I installed all necessary tools. However for some of then such as BWA, Bowtie,... it's usually needed to create indexes. Where should I store those indexes? In the galaxy directory or in each tool directory? How can I tell galaxy where the indexes are? I find a manual's page talking about it / http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup), suggesting to organize the various index files for each build, but I don't know if these folders should be stored into Galaxy directory (eg. in tool-data directory) or what. Could you please explain this a little? Thank you and regards, Rafa Hernández de Diego Genomics of Gene Expression Lab. Bioinformatics and Genomics Department Centro de Investigación Príncipe Felipe (CIPF) C/ Eduardo Primo Yúfera 3 46012 Valencia, Spain ___ 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] Galaxy Local Installation Issue
Dear Galaxy, I had galaxy installed locally, and when I try running tophat, there is no reference genome to select, and it says If your genome of interest is not listed, contact the Galaxy team(below), I was wondering how I would go about solving this issue. Best, Blake Haas Select a reference genome: If your genome of interest is not listed, contact the Galaxy team ___ 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/
