User: gkuffel22

gravatar for gkuffel22
gkuffel22170
Reputation:
170
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Location:
United States
Last seen:
3 months, 2 weeks ago
Joined:
3 years, 6 months ago
Email:
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Laboratory Mgr. at Loyola Genomics Facility, providing a cost effective sample to data solution.

Posts by gkuffel22

<prev • 57 results • page 1 of 6 • next >
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Comment: C: Samtools error assoicated with multiple mapping tools
... I'm not sure if this helps or is related but I see this information on the running log that I keep open when I start our Galaxy server: galaxy.tools WARNING 2018-04-27 10:00:37,920 [p:21025,w:0,m:0] [MainThread] Tool __SORTLIST__: a when tag has not been defined for 'sort_type (sort_type) --> ...
written 3 months ago by gkuffel22170
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Comment: C: Samtools error assoicated with multiple mapping tools
... I cannot reproduce these errors on the public server. This problem is only occurring on our local. We are indeed running version 18.01 of Galaxy. Here are the versions of the tools as shown in "Manage Dependencies": HISAT2 /data/galaxy/galaxy/database/dependencies/_conda/envs/mulled-v1-3b104c ...
written 3 months ago by gkuffel22170
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Samtools error assoicated with multiple mapping tools
... Hoping for some help here. I am having issues with several mapping tools that utilize samtools and I think I have finally identified some commonality between the errors. I will list the errors below. I suspect my issue is something with samtools, however if I look under "Mange Dependencies" all of ...
hisat2 galaxy bwa written 3 months ago by gkuffel22170 • updated 3 months ago by Jennifer Hillman Jackson25k
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Comment: C: Error adding new table to tool_data_table_conf.xml
... Hi Jen, Yes, your link you provided in my previous post was extremely helpful and I am installing hisat indices using the Data Manager as we speak! I just wanted to have a thorough knowledge of how to do this manually as well. I also suspected a format issue but I don't know how that could be as I ...
written 3 months ago by gkuffel22170
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Error adding new table to tool_data_table_conf.xml
... Hi friends, I am trying to add a genome to hisat2 and all is going well except when I try to add the new table info to the bottom of tool_data_table_conf.xml and then I restart the Galaxy server I get the following error: Error parsing file ./config/tool_data_table_conf.xml ParseError: jun ...
galaxy managers install data admin written 3 months ago by gkuffel22170 • updated 3 months ago by Jennifer Hillman Jackson25k
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(Closed) Adding a reference genome to a local Galaxy
... Hoping to find some Galaxy Dev team experts. I am trying to add hg38 to the HiSat2 tool so that the genome is built in. I have followed the tutorial located at: https://galaxyproject.org/admin/data-integration/ Here are the steps I followed: 1. I used HiSat2 through the command line to create the ...
hisat2 fetch galaxy data-managers genome written 3 months ago by gkuffel22170 • updated 3 months ago by Jennifer Hillman Jackson25k
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Comment: C: Using Conda to resolve dependencies
... Ah, that makes much more sense. I am used to seeing variables like this $tool_dependency_dir instead of encapsulated in < >. So my next question would be, do I have to modify the galaxy.yml file to define this variable as I have done below or does this come preconfigured? # Path to th ...
written 4 months ago by gkuffel22170
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Comment: C: Using Conda to resolve dependencies
... I guess that is my big problem. I don't know how to change directories into /_conda. I do see conda installed at this path: /home/galaxy/galaxy/database/dependencies ...
written 4 months ago by gkuffel22170
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Comment: C: Galaxy fatal error running Cutadapt
... Hi Jen, Thanks for the input. Actually I have two separate instances of Galaxy, one on Jetstream and one running on our servers through a virtual machine. I can't control the version of the instance on Jetstream but we have the newest version running on our servers. Point is, I have different probl ...
written 4 months ago by gkuffel22170
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Using Conda to resolve dependencies
... Hi, Do I need to change the galaxy.yml file to enable Conda? As I understood it the newer versions of Galaxy would be preconfigured to use Conda. I have read all of the documentation at docs.galaxyproject.org but maybe I am confused with replacing the default with my own path? I see a directory , b ...
local galaxy conda tool dependencies written 4 months ago by gkuffel22170 • updated 4 months ago by Jennifer Hillman Jackson25k

Latest awards to gkuffel22

Popular Question 4 months ago, created a question with more than 1,000 views. For TopHat and Microbial RNASeq
Popular Question 15 months ago, created a question with more than 1,000 views. For Adding reference genomes to local instance of Galaxy
Popular Question 15 months ago, created a question with more than 1,000 views. For Running TopHat2 with a GTF file
Popular Question 15 months ago, created a question with more than 1,000 views. For Uploading multiple FastQ files from BaseSpace to Galaxy
Popular Question 15 months ago, created a question with more than 1,000 views. For Fasta Files from FTP sites
Popular Question 15 months ago, created a question with more than 1,000 views. For Adding read group information in a bam header
Scholar 16 months ago, created an answer that has been accepted. For A: Remove genomes from tool drop down menus
Popular Question 16 months ago, created a question with more than 1,000 views. For Adding reference genomes to local instance of Galaxy using Rsync
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Trimming Adapters for Illumina Small RNA Libraries
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Uploading multiple FastQ files from BaseSpace to Galaxy
Autobiographer 2.6 years ago, has more than 80 characters in the information field of the user's profile.
Student 3.2 years ago, asked a question with at least 3 up-votes. For Creating a Workflow for Variant Detection for 200 samples

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