Moderator: fubar

gravatar for fubar
fubar1.1k
Reputation:
1,090
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Trusted
Location:
Australia
Website:
http://getgalaxy.org/
Scholar ID:
Google Scholar Page
Last seen:
10 months ago
Joined:
9 years, 3 months ago
Email:
r***********@gmail.com

I started out in family medicine in Australia (where it's called "General Practice") for a decade; became a tenured academic teaching biostats/public health/epidemiology for 15 years; moved to Boston as an independent NIH/CDC supported researcher running a small bioinformatics lab at Harvard for 12 years; returned to Australia about 3 years ago to lead a molecular biology core, doing analyses and developing tools for an epigenetics lab and a lipidomics lab at the Baker IDI in Melbourne. If I seem grumpy, it's probably because I am. At my age, I feel entitled so please bear with me.

Posts by fubar

<prev • 123 results • page 1 of 13 • next >
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Answer: A: can't access data managers
... Assuming you're using the latest, stable release, it's been changed to the "local data" entry below the heading "data" in the admin menu. ...
written 10 months ago by fubar1.1k
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Comment: C: Setting up graphical Galaxy on a Cloud/SERVER
... > we are told that we can access Galaxy at 127.0.0.1:8080. Change localhost (127.0.0.1) in the server configuration to the current local network ip of the server and restart galaxy. Assuming the server firewall allows it, local network workstations should be able to access the server. The defa ...
written 13 months ago by fubar1.1k
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Comment: C: HTML output directory question
... ok - so that old difference between extra_files_path and files_path has been resolved - that's good! At completion of a job, galaxy moves things from the transient job working directory to permanent storage as you've noticed. That means tools can happily spew out temporary messy stuff to that trans ...
written 22 months ago by fubar1.1k
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Answer: A: HTML output directory question
... Try $html_file.extra_files_path in that command line ?  ...
written 22 months ago by fubar1.1k
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Answer: C: How to obtain up/down regulation column for DEG edgeR results
... edgeR is a Bioconductor package so the Bioconductor package support site https://support.bioconductor.org/ is a better place to search for an answer and if necessary, post your question, than here on a Galaxy forum. The edgeR package maintainers hang around there and answer (good) questions readily ...
written 23 months ago by fubar1.1k
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Answer: C: random error : a possible ram problem?
... If the instance is using sqlite, maybe try the same workflow with postgresql as the backend. A docker image makes this test a lot easier - eg: https://github.com/bgruening/docker-galaxy-stable comes with postgres already configured.  ...
written 23 months ago by fubar1.1k
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Answer: A: p-value and FDR
... tl;dr A tiny p value allows you to confidently reject the null hypothesis of no difference. It doesn't really matter much how tiny. Once the FDR is below 0.05, you reject. Ignoring the complexities of interpreting such a value, it depends. With (eg) R,  an architecture specific limit (eg 2.225074e- ...
written 23 months ago by fubar1.1k
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Comment: C: Two instances on different server with only one postgres database ?
... Not that I am aware of. A single instance can be scaled up to cope with thousands of users (eg usegalaxy.org), but each instance must have exclusive control of a complete set of database tables. There was discussion of "federated" Galaxy instances but I'm not sure anyone has working code yet. Send c ...
written 24 months ago by fubar1.1k
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Comment: C: Two instances on different server with only one postgres database ?
... Each Galaxy instance must have an independent set of tables otherwise they will stomp all over each other and cause serious problems. Of course, one single postgresql server can support more than one database but every independent Galaxy instance requires a separate database (eg galProd and galTest) ...
written 2.0 years ago by fubar1.1k
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Answer: A: Where can I find the FastQC tool on the Galaxy webpage?
... Is http://usegalaxy.org the Galaxy instance you are having trouble with? I can see it there right now...Try typing "fastqc" into the search bar at the top of the tool panel on the left of the screen where it says "search tools" ?   ...
written 2.6 years ago by fubar1.1k

Latest awards to fubar

Scholar 2.7 years ago, created an answer that has been accepted. For A: LPED and PBED formats (PLINK)
Centurion 2.9 years ago, created 100 posts.
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: How to uninstall tool?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: add test-data folder in repository of tool shed
Scholar 3.2 years ago, created an answer that has been accepted. For A: add test-data folder in repository of tool shed
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: add test-data folder in repository of tool shed
Scholar 3.2 years ago, created an answer that has been accepted. For A: add test-data folder in repository of tool shed
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Error in BETA basic in Cistrome
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Error in BETA basic in Cistrome
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: what is the differences between GigaGalaxy and Galaxy?Why upload data in GigaGal
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: tgz file uploading and supporting
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: tgz file uploading and supporting

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