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## qiime_centos.md

      
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                / qiime_centos.md
            
            
              Last active
              September 3, 2015 13:35
                — forked from alanorth/qiime_centos.md
            
              
                Manually installing QIIME 1.8.0 on CentOS 6.5...
              
          
    QIIME 1.8.0 on CentOS 6.5

Installing QIIME manually in it's own prefix on CentOS 6.5.  Our cluster has a network-mounted applications directory, so I wanted to install it once there, so all cluster nodes could use it.

Reference: http://qiime.org/install/install.html

Python 2.7.3

QIIME wants this specific version, so let's compile and install it into the qiime/1.8.0 prefix.
Prepare Python source:

  
## galaxy-init-example
#!/bin/bash

#--- config

SERVICE_NAME=galaxy
RUN_AS=galaxy
RUN_IN=/your/galaxy/directory

#--- main actions

## gunicorn_start.bash
#!/bin/bash

NAME="hello_app"                                  # Name of the application
DJANGODIR=/webapps/hello_django/hello             # Django project directory
SOCKFILE=/webapps/hello_django/run/gunicorn.sock  # we will communicte using this unix socket
USER=hello                                        # the user to run as
GROUP=webapps                                     # the group to run as
NUM_WORKERS=3                                     # how many worker processes should Gunicorn spawn
DJANGO_SETTINGS_MODULE=hello.settings             # which settings file should Django use
DJANGO_WSGI_MODULE=hello.wsgi                     # WSGI module name

## conda-r.md

      
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              February 12, 2021 18:12
            
              
                How to install R 3.2.2 using a conda environment on CentOS
              
          
    Download Miniconda


Python 2.7
# 32 bits
$ wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86.sh
# 64 bits
$ wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh


## conda-caRpools.md

      
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              August 18, 2016 19:17
            
              
                Install caRpools on Linux using Conda
              
          
    Create a conda environment to be used with caRpools

$ conda create -n carpools -y pip

Activate the new env

$ source activate carpools


## pvac-seq.md

      
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                adefelicibus
                / pvac-seq.md
            
            
              Created
              September 21, 2016 20:36
            
              
                Install pvac-seq on Ubuntu 
              
          
    Install dependecies

$ sudo apt-get install mysql-server mysql-client mysql-common libmysqlclient-dev
$ sudo apt-get install build-essential git-core cmake zlib1g-dev libncurses-dev patch
$ sudo apt-get install samtools
Create a new enviromnent to pvac-sec


## install-samtools-bcftools-and-htslib.md

      
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                adefelicibus
                / install-samtools-bcftools-and-htslib.md
            
            
              Last active
              April 3, 2024 20:49
            
              
                Install samtools, bcftools and htslib on linux
              
          
    Install Samtools, BCFTools and htslib on linux

Install some build dependencies

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev
[samtools]


## split-vcf-by-sample.sh
for file in *.vcf*; do
  for sample in `bcftools view -h $file | grep "^#CHROM" | cut -f10-`; do
    bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file
  done
done

## ensembl_vep_86_with_offline_cache.md

      
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                adefelicibus
                / ensembl_vep_86_with_offline_cache.md
            
            
              Created
              October 30, 2017 10:16
                — forked from ckandoth/ensembl_vep_86_with_offline_cache.md
            
              
                Install Ensembl's VEP v86 with various caches for running offline
              
          
    Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.
To follow these instructions, we'll assume you have these packaged essentials installed:
## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

  
## Download Google Drive files with WGET
Download Google Drive files with WGET

Example Google Drive download link:

https://docs.google.com/open?id=[ID]
To download the file with WGET you need to use this link:

https://googledrive.com/host/[ID]

Example WGET command:
	#!/bin/bash

	#--- config

	SERVICE_NAME=galaxy
	RUN_AS=galaxy
	RUN_IN=/your/galaxy/directory

	#--- main actions
	#!/bin/bash

	NAME="hello_app" # Name of the application
	DJANGODIR=/webapps/hello_django/hello # Django project directory
	SOCKFILE=/webapps/hello_django/run/gunicorn.sock # we will communicte using this unix socket
	USER=hello # the user to run as
	GROUP=webapps # the group to run as
	NUM_WORKERS=3 # how many worker processes should Gunicorn spawn
	DJANGO_SETTINGS_MODULE=hello.settings # which settings file should Django use
	DJANGO_WSGI_MODULE=hello.wsgi # WSGI module name
	for file in .vcf; do
	for sample in `bcftools view -h $file \| grep "^#CHROM" \| cut -f10-`; do
	bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file
	done
	done
	Download Google Drive files with WGET

	Example Google Drive download link:

	https://docs.google.com/open?id=[ID]
	To download the file with WGET you need to use this link:

	https://googledrive.com/host/[ID]

	Example WGET command: