Hi Galaxy team,
We find that Galaxy workflow is much more convenient and operable for biodata
analysing.Now we get an idea about integrating our Galaxy workflow as a tool in
Galaxy,such as RNAdenovo,Chip-seq,and so on.We do not know whether some other
Galaxy try the same or not ,and whether it
Hi,
Fortunately,I get the human_g1k_v37.fasta.gz in
ftp://ftp.ncbi.nih.gov/1000genomes/ftp/technical/reference/ .
shenwiyn
发件人： shenwiyn
发送时间： 2013-09-05 10:03
收件人： galaxy-dev
主题： Can not find hg_g1k_v37.fa.
Hi everyone,
I want to use the hg_g1k_v37.fa on my local Galaxy,but I can not find
Hi Hans-Rudolf,
Apologies for the delay.Thank you very nuch for your help.My problem solved
successfully after 'smtp_server' settings in my "universe_wsgi.ini" file.
shenwiyn
From: Hans-Rudolf Hotz
Date: 2013-07-31 23:40
To: shenwiyn
CC: galaxy-dev@lists.bx.psu.edu
Subj
Galaxy Tearm,
I use "Select" in "Filter and Sort" to sort my sam file in my local Galaxy.But
I got "no peek " under "Matching pattern: ^@" ,while I got the same sam file
under "NOT Matching pattern: ^@" .Actually,I can got the correct results in
Galaxy main,I don't know what happened to my loca
Hi everyone,
I want to use the hg_g1k_v37.fa on my local Galaxy,but I can not find this
data.When I use the command :
rsync -avzP
rsync://datacache.g2.bx.psu.edu/indexes/hg_g1k_v37/seq/hg_g1k_v37.fa
the error occurred:
receiving incremental file list
rsync: link_stat "/hg_g1k_v37/seq/hg_g1k_v37
Hi ,
I found that the visualization of Circos works greatly in Galaxy main,but
failed on my local Galaxy.I want to find out some information about
configuring and setting up the Circos on local Galaxy,I saw nothing in
http://wiki.galaxyproject.org/New%20Visualization%20Page#Circos_plot_.28aka_C
pt.py
Further more when I want to kill my jobs by clicking in galaxy web,the job
keeps on running in my background.I do not know how to fix this.
Any help on this would be grateful.Thank you very much.
shenwiyn
From: Jurgens de Bruin
Date: 2013-08-07 19:55
To: galaxy-dev
Su
Hi Hans-Rudolf,
Thank you very much for you help.Actually I want some more information about
how to configure 'smtp_server' in "universe_wsgi.ini".Could you show me some
samples to have a look please?
Regards, shenwiyn
From: Hans-Rudolf Hotz
Date: 2013-07-31 23:40
To:
scripts/drmaa_external_killer.py
scripts/external_chown_script.py
Could anyone give me some help please?Thank you.
shenwiyn<>___
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Hi,
I think you can get reference genomes from UCSC,and then make Bowtie2 index
data by bowtie2-build.Other way you can try rsync to get the index files ,for
more information you can see
http://wiki.galaxyproject.org/Admin/Data%20Integration .
Hope to help you.
shenwiyn
From: Gerald Bothe
b)In my background,I get the "qstat" result :
Job idName UserTime Use S Queue
- --- - -
46.server ...n...@genomics.cn galaxy 00:00:00 R batch
sh
Hi everyone,
In my local Galaxy,when I want to reset my Login password,some error occurre
:"Mail is not configured for this Galaxy instance. Please contact an
administrator. "Could anyone tell me some imformation about how to configure
the mail for my Galaxy instance?
Thank you very much.
sh
Hi Carlos,
Thank you very much for your help.I use Galaxy with the torque2.5.0,pbs_python
for a test.It seems to work successfully !
shenwiyn
From: Carlos Borroto
Date: 2013-07-10 01:49
To: shenwiyn
CC: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Build the Galaxy under Cluster
Hi shenwyn
I saw http://wiki.galaxyproject.org/Admin/Config/Jobs about this,but I am not
sure above.Could you help me please?
shenwiyn
From: Thon Deboer
Date: 2013-07-18 14:31
To: galaxy-dev
Subject: [galaxy-dev] Jobs remain in queue until restart
Hi,
I have noticed that from time to time, the job queue seems to be “
Hi everyone，
I am a newer in Galaxy. I installed my Galaxy with Torque2.5.0 . I used my
job_conf.xml for a test ,my Galaxy seems to work with TORQUE by the interface
of pbs_modoule ( _pbs.so) successfully.
In my test job_conf.xml , it seems that we should use collection of
to specify bwa to ru
Hi Carlos,
Thank you very much for your help.I use Galaxy with the torque2.5.0,pbs_python
for a test.It seems to work successfully !
shenwiyn
From: Carlos Borroto
Date: 2013-07-10 01:49
To: shenwiyn
CC: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Build the Galaxy under Cluster
Hi shenwyn
I saw http://wiki.galaxyproject.org/Admin/Config/Jobs about this,but I am not
sure above.Could you help me please?
shenwiyn
From: Thon Deboer
Date: 2013-07-18 14:31
To: galaxy-dev
Subject: [galaxy-dev] Jobs remain in queue until restart
Hi,
I have noticed that from time to time, the job queue seems to be “
Hi everyone,
I want to install my local Galaxy under the Cluster with TORQUE.I have a
question about how they work together successfully.In addition,after my local
Galaxy and TORQUE install successfully,anything else should I do to the Cluster
Galaxy?Thank you very much.
shenwiyn
Hi everyone,
I want to install my local Galaxy under the Cluster with TORQUE.I have a
question about how they work together successfully.In addition,after my local
Galaxy and TORQUE install successfully,anything else should I do to the Cluster
Galaxy?Thank you very much.
shenwiyn
Hi everyone,
I installed my local galaxy successfully.But I have a problem about how to find
out the log in information of each user ,such as the register mail and the
password .And which files do this informations saved?
Thank you!
shenwiyn
Hi everyone,
I have installed GATK tools in my local galaxy .But when I want to test whether
they work successfully ,something error appear:
The error appears under the BAM files we input : Unspecified genome build,
click the pencil icon in the history item to set the genome build
Could anyone te
bowtie-0.12.8 ,we should get rid of Bowtie2,and the same as tophat/tophat2,and
if we keep all of the functions ,all of these we need to installed,right?
shenwiyn
From: greg
Date: 2013-02-22 01:22
To: Jennifer Jackson
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem running
Hi everyone,
I have some questions about the tool of Megablast in NGS:Mapping when I
download the needed indexes .
There are four indexes files we need for Megablast:htgs 28-Jan-2013 ,nt
28-Jan-2013,wgs 28-Jan-2013,phiX174;but there are too many types of the indexes
file in ftp://ftp.ncbi.nlm.ni
Hi,
I have some questions about the tool of Megablast in NGS:Mapping when I
download the needed indexes .
There are four indexes files we need for Megablast:htgs 28-Jan-2013 ,nt
28-Jan-2013,wgs 28-Jan-2013,phiX174;but there are too many types of the indexes
file in ftp://ftp.ncbi.nlm.nih.gov/bla
me and give me some advice please? Thanks.
shenwiyn
From: Enis Afgan
Date: 2013-03-05 10:38
To: shenwiyn
CC: Rafael Hernández; galaxy-...@bx.psu.edu
Subject: Re: Tools and Data
Correct; certain NSG tools require additional configuration for their indices
(http://wiki.galaxyproject.org/Admin/NGS%
Hi,
I've installed Galaxy in local as what Rafael does.I want to make sure that the
basic functions work successfully just depending on the necessary tools in Tool
dependencies manual,and the NGS tools not only depend on the necessary tools
but also some another needed data(such as indexes,and s
Hi,
I want to install our local Galaxy for more than one users. When I want to
install some tools from tool shed via admin user ,and I followed the
instructions in the follow link:
http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_lo
,I get "502 Bad Gateway".
So what happens? How cat I get the data? Is there another way?
Help me please.
shenwiyn
From: Carl Eberhard
Date: 2013-02-27 22:28
To: Ross
CC: shenwiyn; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] all the data files in .loc files needed to download
questions I concerned about now.I am so thankful
for some of you advice.
Thank you very much.
shenwiyn
From: Carl Eberhard
Date: 2013-02-23 02:42
To: shenwiyn
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hello shenwiyn
Hi all,
Are all the data files in .loc files needed to download and put to the right
directory when we install our local galaxy?
thaks
shenwiyn
shenwiyn___
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