Admin: nitesh.turaga

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nitesh.turaga140
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Posts by nitesh.turaga

<prev • 24 results • page 1 of 3 • next >
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Comment: C: ensemblVEP: "Ensembl VEP is not installed in your path."
... Hi, Is your goal here to use `ensemblVEP` as a package inside a Docker image? Or is it to build your own Docker image which uses bioconda to install `ensembleVEP`? If it is the first one, then I suggest you use a different base image, (this is a temporary suggestion) ``` FROM bioconductor/bioc ...
written 3 months ago by nitesh.turaga140
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Comment: C: List of Deprecated Package Bioc 3.9
... Package `miRsponge` has been deprecated in favor of `miRspongeR`. This is a name change as requested by the maintainer. ...
written 3 months ago by nitesh.turaga140
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Answer: C: Installing BiocParallel package on R.3.4.4
... Please try installing via `biocLite()` which is the Bioconductor recommended way of installing bioconductor packages in R-3.4 ``` source("https://bioconductor.org/biocLite.R") BiocInstaller::biocLite("BiocParallel") ``` https://www.bioconductor.org/install/#Legacy (check out this link for more inf ...
written 3 months ago by nitesh.turaga140
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Comment: C: MAGeCKFlute - Installation
... You have a trailing `)` which doesn't work try this, ``` conda create --name mageck-vispr mageck mageck-vispr python=3 ``` But make sure you have your conda channels set correctly (as given by the bioconda page) Also, it's taking a while on my machine as well. But, i suggest you contact, https: ...
written 3 months ago by nitesh.turaga140
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Comment: C: How can I install DeSeq2 in Jupyter Notebook?
... Hi, It's worth taking a look at Bioconda in this instance. I feel like once you launch a Jupyter notebook. If you have anaconda installed already, and you are trying to to install DESeq2, make sure the list of channels you have set are correct. ``` conda config --add channels defaults conda confi ...
written 3 months ago by nitesh.turaga140
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Answer: A: DEXSeqHTML getListElement GRanges error
... Hi Lance, I guess you can install bioconductor-dexseq==1.24.0 on a new conda environment, and copy the script being run from the tool, and use it within that conda environment? AS you mentioned the script being run is /galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/dexseq/f89c9b25feb4/dexseq/ ...
written 6 months ago by nitesh.turaga140
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Comment: C: Can't push upstream - duplicate commits
... Hi Sam, I took a look at bumphunter. There are a couple of things I wanted to say. First, it seems like this commit was the one creating all the duplicate commits for the package. 718d3d8 Merge with Bioconductor devel brach $$ git show 718d3d8 commit 718d3d87af114f8dc404c3889c673fac861bb84c ...
written 7 months ago by nitesh.turaga140
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Comment: C: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
... The argument you need is `template` param <- BatchtoolsParam(workers=5, cluster="sge", template=template) The template can hold your ncpus information.  There is also an option called `registryargs` where you can pass in the resources you want.  Please check the vignette, https://bioconducto ...
written 8 months ago by nitesh.turaga140
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Comment: C: pintersect using GRangeslist
... Please submit your sessionInfo() and also check BiocManager::biocValid(). Paste outputs of both. ...
written 11 months ago by nitesh.turaga140
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Comment: C: Non-Redundant Edges in Connected Components
... Hi Dario, Maybe you can explain the problem to me a little more. I'm trying to follow the example in the connectedComp help page. This is the graph the example mentions ` con <- file(system.file("GXL/kmstEx.gxl",package="graph"), open="r") km <- fromGXL(con) close(con) km ...
written 12 months ago by nitesh.turaga140

Latest awards to nitesh.turaga

Appreciated 2.3 years ago, created a post with more than 5 votes. For Bioconductor git server is now LIVE!
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Bioconductor git transition BETA phase starts now.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Bioconductor git server is now LIVE!
Scholar 2.3 years ago, created an answer that has been accepted. For A: Access to github repository- how does one know if their ssh public key was accep
Scholar 2.3 years ago, created an answer that has been accepted. For A: Remote rejected after resetting to previous commit

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