User: jkoral

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jkoral100
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Posts by jkoral

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Comment: C: Running DESeq2 inside local Galaxy instance
... Hi all, I have been working with Gina on this and we are using the latest version of Galaxy 18.01 and are strictly using Conda for dependency resolution. But when I go to install DeSeq2, I see all the dependencies are resolved through Conda except bioconductor-deseq2. The version shows None and unde ...
written 4 days ago by jkoral100
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Answer: A: Running DESeq2 inside local Galaxy instance
... Hi all, I have been working with Gina on this and we are using the latest version of Galaxy 18.01 and are strictly using Conda for dependency resolution. But when I go to install DeSeq2, I see all the dependencies are resolved through Conda except bioconductor-deseq2. The version shows None and unde ...
written 4 days ago by jkoral100
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bioconductor-cummerbund dependency will not resolve
... I have installed CuffDiff, but there is a failed dependency called bioconductor-cummerbund that will not resolve. When running a job in CuffDiff, I get the following error message. Conda dependency seemingly installed but failed to build job environment. This is on a local instance and is running v ...
cuffdiff local install conda cummerbund written 7 days ago by jkoral100 • updated 7 days ago by Jennifer Hillman Jackson24k
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Answer: A: FastQC job just keeps running without any output
... I was able to figure it out. Since I installed Ubuntu Server with no graphics, it would not display the results. I installed xauth xorg and xorg-dev and the job ran in about 5 seconds and displayed the output. Thanks again for the quick replies. Joe ...
written 11 days ago by jkoral100
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Answer: A: FastQC job just keeps running without any output
... The problem is, I can run this exact job on another instance, just not this one. It just keep spinning.I added the tool to the whitelist, but it still not produce the results. Thanks. ...
written 11 days ago by jkoral100
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FastQC job just keeps running without any output
... I just installed the latest Galaxy version 18.01 of Galaxy on a virtual machine running Ubuntu. For some reason when I run FastQC, the status show FastQC on data 1: RawData and FastQC on data 1: Webpage are just spinning saying "This job is currently running". It never finishes. The version of FastQ ...
local galaxy html display whitelist written 12 days ago by jkoral100
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Comment: C: Issue installing Galaxy on a local server for a multi-user production environmen
... -I then downloaded the virtualenv.py file ``` wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py ``` Then ``` python virtualenv.py --no-site-packages virtual_env ``` And get ``` [galaxy@HSDMongo1 galaxy]$ python virtualenv.py --no-site-packages virtual_env Traceback (most recent call ...
written 12 months ago by jkoral100 • updated 12 months ago by Martin Čech ♦♦ 4.5k
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Comment: C: Issue installing Galaxy on a local server for a multi-user production environmen
... I am working with Gina on this. I can get the release fine. I just cannot do anything after that. When I try to run sh run.sh, that is when I get that error. Let me add that I am using CentOS 6.7 along with the version 2.6.6 of Python (since yum needs it). When logged on as a galaxy user, I have .b ...
written 12 months ago by jkoral100 • updated 12 months ago by Martin Čech ♦♦ 4.5k
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Quick overview of downloading genomes to local galaxy
... Can someone give me a quick overview of what is needed to download and setup genomes on a local galaxy instance. I have rsync'd the genomes that the Biostatistician requested, but it looks like I need to download some location files, etc. I see a lot on the Wiki pages, but am unclear on what exactl ...
genomes rsync galaxy local written 3.1 years ago by jkoral100 • updated 3.1 years ago by Jennifer Hillman Jackson24k
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Comment: C: How to organize list of Tools on local galaxy
... Thanks so much. ...
written 3.1 years ago by jkoral100

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to organize list of Tools on local galaxy
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