User: Vimalkumar Velayudhan
Vimalkumar Velayudhan • 200
- Reputation:
- 200
- Status:
- Trusted
- Location:
- Ireland
- Website:
- https://vimal.io/
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 year, 2 months ago
- Joined:
- 9 years, 11 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
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... You are probably trying to open gedit from the terminal using sudo/root.
You could use a command line text editor like **nano**. Alternatively,
you can try creating the configuration file with your regular user account and then copy it over to the final location using **sudo** ...
written 14 months ago by
Vimalkumar Velayudhan • 200
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... This is a method I followed to get an organism's complete lineage from [NCBI][1] taxonomy data. The procedure involves:
1. Creating a MySQL database.
2. Initialising the database with the [BioSQL][2] schema.
3. Downloading and importing the NCBI taxonomy data into the database.
4. Using a python sc ...
written 2.1 years ago by
Vimalkumar Velayudhan • 200
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... Did you use the same password in the config file i.e., the password used while creating the orthomcl user?
If it still doesn't work, please post your complete orthomcl.config file. You can remove the password setting. ...
written 2.1 years ago by
Vimalkumar Velayudhan • 200
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... There needs to be a `dbVendor=mysql` setting in addition to the `dbConnectString=...` in the config file. If you had created the configuration file by copying the orthomcl.config.template, this should already be present. ...
written 2.1 years ago by
Vimalkumar Velayudhan • 200
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... You haven't mentioned what Linux distribution this is. If you are on a Debian/Ubuntu system, you need to install the system library that python-lzo requires i.e., **liblzo2-dev**. On RPM based systems like Fedora or openSUSE, this package is most likely named **lzo2-devel**. ...
written 2.2 years ago by
Vimalkumar Velayudhan • 200
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... Cutadapt has minimal dependencies so with Python 3, you could also do the
following assuming the python3-venv module is installed:
# install latest version
python3 -m venv cutadapt
source cutadapt/bin/activate
pip install cutadapt
deactivate
# install version 1.14
pyt ...
written 2.2 years ago by
Vimalkumar Velayudhan • 200
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... 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 2.3 years ago by
Vimalkumar Velayudhan • 200
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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 2.3 years ago by
Vimalkumar Velayudhan • 200
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... 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 2.3 years ago by
Vimalkumar Velayudhan • 200
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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 2.3 years ago by
Vimalkumar Velayudhan • 200
Latest awards to Vimalkumar Velayudhan
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For How to - Install Python packages in a virtual environment (virtualenv)
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For OrthoMCL installation on Ubuntu Linux
Appreciated
2.4 years ago,
created a post with more than 5 votes.
For OrthoMCL installation on Ubuntu Linux
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: ClustAGE error on Linux - "Support directory 'bin' is not present"
Autobiographer
3.2 years ago,
has more than 80 characters in the information field of the user's profile.
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