User: Marco Blanchette

Reputation:
10
Status:
New User
Location:
United States
Last seen:
4 years, 5 months ago
Joined:
4 years, 6 months ago
Email:
m**@stowers.org

Posts by Marco Blanchette

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Problem with toolshed installed deepTools on CloudMan instance
... You probably meant to say /mnt/galaxy/galaxy-app/tool-data/shared/ucsc/ucsc_build_sites.txt, right?  In fact, on the CloudMan instance there is none... there is  /mnt/galaxy/galaxy-app/tool-data/shared/ucsc/ucsc_build_sites.txt.new and  /mnt/galaxy/galaxy-app/tool-data/shared/ucsc/ucsc_build_sit ...
written 4.5 years ago by Marco Blanchette10
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Problem with toolshed installed deepTools on CloudMan instance
... I successfully installed deepTools using the toolShed from the Galaxy main repos. The problem is that when users try to do analysis with deepTools, they always get the following message:  ERROR: Unable to read builds for site file /mnt/galaxy/galaxy-app/lib/galaxy/util/../../../tool-data/shared/ucs ...
cloudman galaxy software error written 4.5 years ago by Marco Blanchette10 • updated 4.4 years ago by Jennifer Hillman Jackson25k
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Comment: C: Using Data Managers for uploading new genome
... You'll find that interesting... the history tab turns green, thumb up! but if you open the tab and look at view data, this is what's in window: ERROR: Unable to read builds for site file /mnt/galaxy/galaxy-app/lib/galaxy/util/../../../tool-data/shared/ucsc/ucsc_build_sites.txt This is why I was ve ...
written 4.5 years ago by Marco Blanchette10
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Comment: C: Using Data Managers for uploading new genome
... Dannon, not sure this is per design but, I went in and added the following line to the tool-data/shared/ucsc/builds.txt file using the following command line: sudo echo 'sacCer3 S. cerevisiae Apr. 2011 (SGD/sacCer3) (sacCer3)' >> /mnt/galaxy/galaxy-app/tool-data/shared/ucsc/builds.txt Restar ...
written 4.5 years ago by Marco Blanchette10
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Comment: C: Using Data Managers for uploading new genome
... As a side note, the bowtie2 data manager works great to populate bowtie2/tophat2 with indices from genomes in the drop down menu!!! I wish I could set the download volume as I am filling my data volume with files that could be located elsewhere... (I did some poking around to see how difficult it wo ...
written 4.5 years ago by Marco Blanchette10
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Comment: C: Using Data Managers for uploading new genome
... Since the genome in not in the drop box panel from the tool (my understanding is that this is populated from the tool-data/shared/ucsc/builds.txt file). I tried filling in the input with info (putting sacCer3 everywhere) or not entering anything. Same result, here is the error from the history ERRO ...
written 4.5 years ago by Marco Blanchette10
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Using Data Managers for uploading new genome
... I just put in production a small CloudMan based Galaxy server for our institute and in addition to specific tools that some users requested, there is a need to install some genome files and indices not present on the vanilla server. Precisely, I am trying to install the fasta for the UCSC version of ...
cloudman galaxy data managers written 4.5 years ago by Marco Blanchette10 • updated 4.5 years ago by Dannon Baker3.7k
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Comment: C: Problem installing fastq groomer from ToolShed on CloudMan instance
... Same for me... Still trying to figure out what's wrong with the other instance... One issue though... I was unable to specify a new panel section on either the new or the old instances. For examples, I couldn't put the bedtools in a bedtools section, everything appear at the end of the menu (also, ...
written 4.5 years ago by Marco Blanchette10
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Answer: A: Problem installing fastq groomer from ToolShed on CloudMan instance
... Hmm... I'm a bit clueless as what is going on... Python is working fine, running version 2.7.3. I'm not a python person so i can't really easily test anything... But I did restart the server and now I'm getting a different error   Tool dependency status:Error Tool dependency installation error:Th ...
written 4.5 years ago by Marco Blanchette10
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Problem installing fastq groomer from ToolShed on CloudMan instance
... Dear all, I've been trying to install tools on my brand new CloudMan Galaxy instance using toolshed. I am trying to install Fastq Groomer and I am getting errors related to galaxy_sequence_utils. Am'I doing something wrong? Here is the error log from that dependency from the admin tool management p ...
cloudman galaxy tools written 4.5 years ago by Marco Blanchette10

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