Admin: Martin Čech

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Martin Čech ♦♦ 4.5k
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United States
Twitter:
martenson
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Last seen:
2 days, 22 hours ago
Joined:
4 years, 4 months ago
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m*****@bx.psu.edu

Galaxy Team member

Posts by Martin Čech

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Answer: A: using 0% but I have files and jobs not running
... On Main Galaxy, since it is a free public service, the job may be queued for hours before it starts running. Your second point suggest that you actually do not have any data on your account. ...
written 15 days ago by Martin Čech ♦♦ 4.5k
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Answer: C: Disk Quota space management in Galaxy
... Are you talking about the main Galaxy at usegalaxy.org? If so have a look here: https://galaxyproject.org/support/account-quotas/#i-purged-but-still-need-more-space ...
written 15 days ago by Martin Čech ♦♦ 4.5k
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Answer: A: Automated Galaxy Installation: ephemeris or bioblend?
... 1. yes, see [master_api_key](https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L1421) in config 1. yes, the install tools playbook (or using ephemeris directly) are the recommended way afaik ...
written 16 days ago by Martin Čech ♦♦ 4.5k
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Answer: A: Download files from galaxy using bash (curl/wget)
... For dataset collections and datasets within collections you have to supply your API key with the request. You can add it to the end of the collection download url, the command would look something like this: $ wget https://usegalaxy.org/api/dataset_collections/d20ad3e1ccd4595de/download?key=MYSECRE ...
written 17 days ago by Martin Čech ♦♦ 4.5k
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Answer: A: safari can't connect to the server "localhost".
... The [config sample](https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L21) says: > Use ':8080' to listen on all available network interfaces. So I think you shouldn't be adding the 0.0.0.0 part. Don't forget to restart, as Devon says. ...
written 17 days ago by Martin Čech ♦♦ 4.5k
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Answer: A: How to download a batch consisting of 50 bam files, using CURL or wget
... For dataset collections and datasets within collections you have to supply your [API key](https://galaxyproject.org/develop/api/#enabling) with the request. You can add it to the end of the collection download url, the command would look something like this: `$ wget https://usegalaxy.org/api/datase ...
written 17 days ago by Martin Čech ♦♦ 4.5k
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Answer: A: ERROR+HELP+URGENT: vcffilter removed. Why? Put it back please
... The new version of the vcffilter tool is available. It behaves a bit different so you might need to adjust your workflows. https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy1 ...
written 25 days ago by Martin Čech ♦♦ 4.5k
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Comment: C: Private vs Public Galaxy: different outcomes following Fastq upload
... Thanks for reporting this, I made an issue for it at https://github.com/galaxyproject/cloudlaunch/issues/140 so the responsible people can analyse it. Feel free to add any details you know there. ...
written 27 days ago by Martin Čech ♦♦ 4.5k
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Comment: C: Private vs Public Galaxy: different outcomes following Fastq upload
... I just learned that you can use the latest GVL image instead of the CloudMan and it has Galaxy 17.09 included - https://launch.usegalaxy.org/catalog/appliance/genomics-virtual-lab ...
written 28 days ago by Martin Čech ♦♦ 4.5k
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Comment: C: Private vs Public Galaxy: different outcomes following Fastq upload
... Sorry, I forgot you are on cloudman. I think cloudman instances are not easily updateable until the new cloudman release is published, so proper setting of datatype is your best option now. fastqsanger.gz is also available only since 17.09 so you have to make due with just `fastqsanger`. Galaxy will ...
written 28 days ago by Martin Čech ♦♦ 4.5k

Latest awards to Martin Čech

Scholar 17 days ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 25 days ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 28 days ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 7 weeks ago, created an answer that has been accepted. For A: the storage problem
Scholar 7 weeks ago, created an answer that has been accepted. For A: the storage problem
Scholar 9 weeks 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: How to uninstall package which not appear in installed tools menu?
Teacher 4 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 4 months ago, created an answer that has been accepted. For A: How to uninstall package which not appear in installed tools menu?
Scholar 5 months ago, created an answer that has been accepted. For A: How to uninstall package which not appear in installed tools menu?
Teacher 5 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 7 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Change colour of datasets in the history pane?
Scholar 14 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Scholar 14 months ago, created an answer that has been accepted. For A: R tool in galaxy
Scholar 14 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Scholar 15 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Teacher 18 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 18 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Teacher 19 months ago, created an answer with at least 3 up-votes. 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 19 months ago, created an answer with at least 3 up-votes. For A: Change colour of datasets in the history pane?
Scholar 20 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Creating Appropriate Tool Dependencies for Custom Tool in Galaxy

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