Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format) from the archive. fastq-dump...to put things into FASTQ for further processing. The --split-files part of the comma...1559 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh % Total % R...1555 days ago
Bash command to install Miniconda !
(base) [wsu29@bladeamd-2 tmp]$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh --2020-02-01 13:25:25-- https://repo.anaconda.com/miniconda...1555 days ago
Bash command to install bwa, samtools, picard !
(base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata (repodata.json): done Solving environment: - The environment is inconsistent, please c...1555 days ago
Bash command to install GATK, Bedtools and SnpEff !
(my_GATK) [wsu29@bladeamd-2 tmp]$ conda install gatk Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environme...1555 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo] password for...n the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking...1550 days ago
Correct bash command to zip your vcf file
bgzip -c file.vcf > file.vcf.gz tabix -p vcf file.vcf.gz #More at http://www.htslib.org/doc/tabix.html1523 days ago
Exit Bash Script When Any Command Fails
This can actually be done with a single line using the set builtin command with the -e option. #1-------...--------------- # exit when any command fails #Putting this at the t...cause the script to exit if any commands return a non-zero exit code....keep track of the last executed comma...1520 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker docker-engin...ds$ docker Usage: docker [OPTIONS] COMMAND A self-sufficient runtime...on information and quit Management Commands: builder Manage build...AND --help' for more information on a comma...1513 days ago
1507 days ago