Admin: Martin Čech

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Martin Čech ♦♦ 4.8k
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Galaxy Team member

Posts by Martin Čech

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Comment: C: best galaxy app for viewing plink .bed files
... Your best bet probably is to search for a converter that converts it to something that is viewable. e.g. you could use plink to export it in some format more useful to you. ...
written 4 weeks ago by Martin Čech ♦♦ 4.8k
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Comment: C: Galaxy installation fail
... the process is defines by its `id`, you can obtain it by running `ps | grep uwsgi` and noting the first column of the proper row with the process ...
written 4 weeks ago by Martin Čech ♦♦ 4.8k
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Answer: A: satya ranjan singh
... how to work with libraries: https://galaxyproject.org/data-libraries/ read about mapping here: http://galaxyproject.github.io/training-material/topics/sequence-analysis/ ...
written 4 weeks ago by Martin Čech ♦♦ 4.8k
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Comment: C: Galaxy installation fail
... That warning is fine, safe to ignore. As of the stuck process that happens to me from time to time too. MacOS and uwsgi are not very well tested combination. directly `kill -9` the process and start over like Jenn suggested. ...
written 4 weeks ago by Martin Čech ♦♦ 4.8k
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Answer: A: Galaxy installation fail
... quickfix: if you are on 18.05 or newer run this from your galaxy folder `./.venv/bin/pip uninstall -y uwsgi && ./.venv/bin/pip install --no-cache-dir uwsgi==2.0.17` We are aware of this issue on MacOS, you can follow details here:https://github.com/galaxyproject/galaxy/issues/6470 ...
written 4 weeks ago by Martin Čech ♦♦ 4.8k
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Answer: A: Link to dataset (rather than copying)
... > Does this process enable "add datasets to current folder from user directories" to be displayed? yes > I'm assuming on a local instance the reference to "public" are those users who have access to local datasets. No, public is everybody who can reach the Galaxy instance. ...
written 4 weeks ago by Martin Čech ♦♦ 4.8k
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Comment: C: Installation of new tools gets stuck on "cloning"
... The 18.09 is an unreleased development version of Galaxy, the current release is 18.05 https://docs.galaxyproject.org/en/master/releases/index.html That said it should work. Do you see anything suspicious in the Galaxy's log? ...
written 4 weeks ago by Martin Čech ♦♦ 4.8k
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Answer: A: administrator e-mail designation through galaxy.yml.sample
... Galaxy has changed its configuration format, so if you set up a new Galaxy, it will run with default settings without any configuration file, even ignoring the samples. If you want to set up an admin account create `galaxy.yml` file and set `admin_user: ` (note the colon instead of equal sign). You ...
written 5 weeks ago by Martin Čech ♦♦ 4.8k
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Comment: C: Installing tools in my Local Galaxy from Tool Shed not working
... Is there anything in the Galaxy's log? That would be in the terminal that you started Galaxy from. Also I would not bother about the GATK2 - it is long deprecated and very outdated - better find newer tools. ...
written 5 weeks ago by Martin Čech ♦♦ 4.8k
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Comment: C: fast qc on fastq.gz files imported from ENA
... The actual exception you are getting is `uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'` which indicates that your file is in a wrong format I think. ...
written 5 weeks ago by Martin Čech ♦♦ 4.8k

Latest awards to Martin Čech

Scholar 5 weeks ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to uninstall package which not appear in installed tools menu?
Scholar 8 weeks ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 8 weeks ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 3 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 3 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 3 months ago, created an answer that has been accepted. For A: the storage problem
Scholar 4 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 4 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 4 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 5 months ago, created an answer that has been accepted. For A: the storage problem
Scholar 5 months ago, created an answer that has been accepted. For A: the storage problem
Scholar 6 months ago, created an answer that has been accepted. For A: the storage problem
Scholar 8 months ago, created an answer that has been accepted. For A: How to uninstall package which not appear in installed tools menu?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to uninstall package which not appear in installed tools menu?
Scholar 8 months ago, created an answer that has been accepted. For A: How to uninstall package which not appear in installed tools menu?
Scholar 9 months ago, created an answer that has been accepted. For A: How to uninstall package which not appear in installed tools menu?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to uninstall package which not appear in installed tools menu?
Scholar 11 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Change colour of datasets in the history pane?
Scholar 18 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Scholar 19 months ago, created an answer that has been accepted. For A: R tool in galaxy
Scholar 19 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Scholar 19 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Change colour of datasets in the history pane?

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