User: Vimalkumar Velayudhan

Reputation:
180
Status:
Trusted
Location:
Ireland
Website:
https://vimal.io/
Scholar ID:
Google Scholar Page
Last seen:
1 day, 13 hours ago
Joined:
7 years, 8 months ago
Email:
c******@vimal.io

Bioinformatics Software Developer & Linux System Administrator

I'm currently developing BioVM - a virtual machine with pre-configured Bioinformatics software.

Previously, I have contributed in the development of software like ITQuery, RiboPlot and riboSeqR wrapper (hosted at RiboGalaxy) and VIGA. Some of this work has been included in scientific publications.

A complete list of the work I have done is available.

Posts by Vimalkumar Velayudhan

<prev • 28 results • page 1 of 3 • next >
2
votes
2
answers
122
views
2
answers
Answer: C: Simple visual output of Pairwise Sequence alignment
... I had implemented something similar in RiboPlot to mark the positions of start and stop codons in three reading frames. This was done using [Matplotlib][1]. Code is on [github][2] and the plot is generated in the [plot_profile][3] function. ![enter image description here][4] [1]: https://matplo ...
written 6 days ago by Vimalkumar Velayudhan180
1
vote
0
answers
94
views
0
answers
Comment: C: Obisilva (obitools) not working
... With obitools version 1.2.11, the `obisilva --ssu --parc` command works fine. You should try again after updating obitools if you have an older version. ...
written 9 days ago by Vimalkumar Velayudhan180
0
votes
1
answer
1.1k
views
1
answers
Comment: C: OrthoMCL installation on Ubuntu Linux
... Your hard disk is full. You could try to free some disk space by removing files you don't need or moving input/output files from previous steps. Another possibility is to move the database directory to a new location with free space i.e., a separate disk partition. Here is a tutorial on how to do th ...
written 19 days ago by Vimalkumar Velayudhan180
0
votes
0
answers
116
views
0
answers
Comment: C: docker container for Pindel
... No problem! `/opt/pindel-0.2.5b8/pindel` argument isn't required as it appears pindel is run by default when starting the container. Looks like pindel2vcf is a separate Docker image https://hub.docker.com/r/mgibio/pindel2vcf ...
written 25 days ago by Vimalkumar Velayudhan180
0
votes
0
answers
116
views
0
answers
Comment: C: docker container for Pindel
... The image on Docker hub doesn't have the *latest* tag which `docker pull` looks for by default. The only available version is [tagged][1] v0.2.5b8. You should be able to pull it using: docker pull mgibio/pindel:v0.2.5b8 [1]: https://hub.docker.com/r/mgibio/pindel/tags/ ...
written 25 days ago by Vimalkumar Velayudhan180
0
votes
1
answer
1.1k
views
1
answers
Comment: C: OrthoMCL installation on Ubuntu Linux
... Sorry I wouldn't be of much help with the usage of the software as I've only performed installation for users in the lab. The SQL error is similar to the one [reported earlier][1] by biodianita. From looking at the orthomclLoadBlast script, it appears both the SUBJECT_ID and QUERY_ID have a 60 cha ...
written 27 days ago by Vimalkumar Velayudhan180
0
votes
1
answer
1.1k
views
1
answers
Comment: C: OrthoMCL installation on Ubuntu Linux
... That entire command should be on a single line: sudo checkinstall --install=no --pkgname orthomcl --pkgversion 2.0.9 --pkgrelease 1 --pkglicense gpl --maintainer "you@email.com" --provides orthomcl --exclude /usr/local/lib/perl/5.18.2/perllocal.pod make install The linebreaks (\\) were added ...
written 29 days ago by Vimalkumar Velayudhan180
1
vote
1
answer
454
views
1
answers
Comment: C: python script error: ImportError: No module named pysam
... You can create a new conda environment with Python 2 and install pysam: conda create -n pysam -c bioconda python=2 pysam=0.9.1 Then, activate that environment and run your script: conda activate pysam python2.7 overlapping_reads.py ...
written 5 weeks ago by Vimalkumar Velayudhan180
1
vote
1
answer
340
views
1
answers
Answer: A: package gwascat is not available for R version 3.4.4
... For the XML package to compile, you will need the xml libraries and header files (`sudo apt install libxml2-dev`) installed. The error message doesn't say that! Other packages might require additional libraries. You could try installing one failing package at a time and once they are installed succe ...
written 6 weeks ago by Vimalkumar Velayudhan180
0
votes
1
answer
337
views
1
answers
Comment: C: how to run bioinformatics tools via docker
... No other changes have been made to the Dockerfile. You can find it [here][1]. The FTP errors indicate a connectivity issue (probably ports blocked in the firewall) from your computer to ftp.ensembl.org. This could also be the reason why the original docker build failed too. As for `fusioncatcher ...
written 6 weeks ago by Vimalkumar Velayudhan180

Latest awards to Vimalkumar Velayudhan

Popular Question 18 days ago, created a question with more than 1,000 views. For OrthoMCL installation on Ubuntu Linux
Appreciated 9 weeks ago, created a post with more than 5 votes. For OrthoMCL installation on Ubuntu Linux
Scholar 5 months ago, created an answer that has been accepted. For A: ClustAGE error on Linux - "Support directory 'bin' is not present"
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 625 users visited in the last hour