BOL: Related items

snakepipes: A toolkit based on snakemake and python for analysis of NGS data

Jit — Thu, 30 May 2019 04:06:13 -0500

snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data.

DNA-mapping*
ChIP-seq*
RNA-seq*
ATAC-seq*
scRNA-seq
Hi-C
Whole Genome Bisulfite Seq/WGBS

(*Also available in "allele-specific" mode)

snakePipes can be installed via conda :

'conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'.

Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online.

Address of the bookmark: https://github.com/maxplanck-ie/snakepipes

Python Mini Projects !

BioStar — Mon, 16 Jan 2023 02:14:03 -0600

There is a directory for each chapter of the book. Each directory contains a test.py program you can use with pytest to check that you have written the program correctly. I have included a short README to describe each exercise. If you have problems writing code (or if you would like to support this project!), the book contains details about the skills you need.

https://github.com/kyclark/tiny_python_projects

Address of the bookmark: https://github.com/kyclark/tiny_python_projects

Fix rewritable error of ELGG !

Abhi — Mon, 15 Nov 2021 06:23:46 -0600

The mod_rewrite module uses a rule-based rewriting engine, based on a PCRE regular-expression parser, to rewrite requested URLs on the fly. By default, mod_rewrite maps a URL to a filesystem path. However, it can also be used to redirect one URL to another URL, or to invoke an internal proxy fetch.

mod_rewrite provides a flexible and powerful way to manipulate URLs using an unlimited number of rules. Each rule can have an unlimited number of attached rule conditions, to allow you to rewrite URL based on server variables, environment variables, HTTP headers, or time stamps.

mod_rewrite operates on the full URL path, including the path-info section. A rewrite rule can be invoked in httpd.conf or in .htaccess. The path generated by a rewrite rule can include a query string, or can lead to internal sub-processing, external request redirection, or internal proxy throughput.

Further details, discussion, and examples, are provided in the detailed mod_rewrite documentation.

sudo a2enmod rewrite

sudo systemctl restart apache2

sudo nano /etc/apache2/sites-available/000-default.conf

Write this

/etc/apache2/sites-available/000-default.conf

<VirtualHost *:80>
    <Directory /var/www/html>
        Options Indexes FollowSymLinks MultiViews
        AllowOverride All
        Require all granted
    </Directory>

    . . .
</VirtualHost>

Address of the bookmark: https://www.digitalocean.com/community/tutorials/how-to-rewrite-urls-with-mod_rewrite-for-apache-on-ubuntu-18-04

swgis v2.0 : a seqword genomic island sniffer

Abhimanyu Singh — Thu, 01 Nov 2018 12:35:52 -0500

swgis v2.0 is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all identified genomic islands were deposited in the eugi database.

download swgis v2.0

Address of the bookmark: http://eugi.bi.up.ac.za/eugi_download_swgis.php