Dear folks,
Could you help me double check if my understanding is correct for EMS density
mapping? For the tool CloudMap: EMS Variant Density Mapping, it does not work
for other species except C.elegans, correct?
For the workflow CloudMap EMS Variant Density Mapping workflow (takes VCF of
Dear folks,
Why could not I find BDGP 5.74 in the drop-down menu of SnpEff? If I want to
use this version, what should I do or what other steps do I need to install it?
Thank you so much!
From: Wang, Xiaofei
Sent: Monday, April 14, 2014 9:50 AM
To: Björn
still can not find it in the menu of SnpEff after downloading and installing it
by the two-steps as below.
Thanks a lot!
Best,
Xiaofei
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Wang, Xiaofei [xfw...@ku.edu]
Sent
Dear there,
I got this error as below when I run CloudMap workflow in local galaxy
instance. What is it the meaning of this error? Is it a general error or
specific one for my data? Thanks a lot! Xiaofei
error
An error occurred with this dataset:
WARNINGS: Some warning were detected
Warning
...@gmail.com]
Sent: Monday, April 14, 2014 8:47 AM
To: Wang, Xiaofei
Cc: Dannon Baker; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy
Hello,
That's a good question! Does the size in the top right change when the page is
reloaded
Dear there,
May I ask a question which might be really simple?
How to delete a dataset from a history in local Galaxy? When I clicked on
delete (x), the size on disk is still the same as before deleting it.
[cid:d28891d2-9d20-4688-8e3e-3bf75caa662e]
Thank you so much!
Best,
Xiaofei
Baker [dannon.ba...@gmail.com]
Sent: Friday, April 11, 2014 4:42 PM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] how to delete datasets or save space on local galaxy
Hi Xiaofei,
The (x) simply flags a dataset for deletion, it does not remove it from disk.
This happens
Yes, it works. But, I am still a little bit confuse about the size on the top
right corner. Why does not it change after purging datasets?
From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Friday, April 11, 2014 4:57 PM
To: Wang, Xiaofei
Cc: galaxy-dev
]
on behalf of Wang, Xiaofei [xfw...@ku.edu]
Sent: Thursday, April 03, 2014 3:52 PM
To: Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Oh, hooray, I figured it out.
what I did is to go to this folder /Users/pablocingolani/snpEff and download
Dear there,
I tried to download workflow and import it into another my local Galaxy
instance. But, when I downloaded and exported it from main Galaxy by Download
to File, it showed as below.
Not Found
The resource could not be found.
No route for
Yes, I really appreciate for your help!
From: emulato...@gmail.com [emulato...@gmail.com] on behalf of Martin Čech
[mar...@bx.psu.edu]
Sent: Friday, April 04, 2014 11:28 AM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Download
Yes, it is figured out when I downloaded the version of 1.1.2. I thought is no
longer available.
Thank you so much!
Best,
Xiaofei
From: Nate Coraor [n...@bx.psu.edu]
Sent: Friday, April 04, 2014 11:20 AM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
Subject
Dear there,
I got this error when I run CloudMap EMS Variant Density Mapping workflow for
Depth of Coverage on the local Galaxy instance on Mac. In fact, it works fine
for Depth of Coverage when I run another workflow (Unmapped Mutant workflow)
locally.
I really appreciate you guys for
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Thursday, April 03, 2014 5:25 AM
To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
After SnpEff Databases Execute
Dear there,
I am still stuck there for FASTQ Summary Statistics. Could you give me some
clues to fix it?
Thanks a lot!
Best,
Xiaofei
From: Wang, Xiaofei
Sent: Wednesday, April 02, 2014 11:21 AM
To: Daniel Blankenberg
Cc: Björn Grüning; galaxy-dev
[galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Wang, Xiaofei [xfw...@ku.edu]
Sent: Thursday, April 03, 2014 10:31 AM
To: Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
1. click SnpEff Download
2. choose one genome from SnpEff Databases
Dear there,
When I run CloudMap EMS Variant Density Mapping workflow (takes VCF of
heterozygous and homozygous variants to subtract) (imported from uploaded file)
on local Galaxy instance, I got this
[X]
, when I wanted to edit the workflow. Also, I got this
The following tools are beinge
Dear there,
When I used SnpEff in local galaxy instance, I got an error:
Exception in thread main java.lang.UnsupportedClassVersionError:
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method) at
[bjoern.gruen...@gmail.com]
Sent: Wednesday, April 02, 2014 10:35 AM
To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Hi Xiaofei,
Dear there,
When I used SnpEff in local galaxy instance, I got an error:
Exception in thread main
return self.nuc_index_base[ column ]
IndexError: list index out of range
From: Daniel Blankenberg [d...@bx.psu.edu]
Sent: Wednesday, April 02, 2014 11:14 AM
To: Wang, Xiaofei
Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff
option value=hg37Human (hg37)option
option value=mm37.61Mouse (mm37.61)option
param
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, April 02, 2014 10:35 AM
To: Wang, Xiaofei; galaxy-dev
12:55 PM
* To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu
* Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
*
* Hi,
*
* that means that the snpeff annotation is missing. You can install it
* with the snpeff datamanager under your Admin panel
: Wednesday, April 02, 2014 4:17 PM
To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Hi Xiaofei,
Dear Bjoern,
As your suggestion, I tried to install the snpEff annotation. But, I think I
am still be stuck there. What I did
[g...@bx.psu.edu]
Sent: Tuesday, March 11, 2014 8:47 AM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool
dependencies)
Hello,
It's difficult to determine the cause of the problem in your environment based
on the details
, March 11, 2014 8:47 AM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool
dependencies)
Hello,
It's difficult to determine the cause of the problem in your environment based
on the details you've provided. If you have defined
Hi folks,
Could anybody answer my question and help me figure it out?
Thank you so much!
Best,
Xiaofei
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Wang, Xiaofei [xfw...@ku.edu]
Sent: Thursday, March 06, 2014 4
Dear there,
I am trying to install some tools from toolshed on my local galaxy instance,
like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and
sam_to_bam. For the first time, I got a warning before installing, something
like this set the value of your tool_dependency_dir
I have the same question. But, I want to use it on Drosophila and use SnpEff
for CloudMap pipeline.
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Clint Christensen [cli...@txbiomedgenetics.org]
Sent: Monday,
Dear,
Is it possible to use SnpEff with genomes of other species (e.g. Drosophila)
other than C.elegan on galaxy website (not local)? It seems the only option for
the genome menu (Caenorhabditis elegants : WS220.64).
In fact, I am trying to use CloudMap (the EMS Variant Density Mapping
, GATK for
calling SNPs, ...) by hand not use the CloudMap pipeline on Drosophila?
Thanks
From: Wolfgang Maier [wolfgang.ma...@biologie.uni-freiburg.de]
Sent: Friday, February 14, 2014 11:48 AM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev
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