Bash script to download SRA file !
...t directly compatible with any downstream tools, so it's necessary to put things into FASTQ for further processing. The --split-files part of the command ensures we get two files, one...1573 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 % Received % Xferd...1569 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/...1569 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 ch...1569 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 ## environmen...1569 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.html1537 days ago
Exit Bash Script When Any Command Fails
...single line using the set builtin command with the -e option. #1----...---------------- # exit when any command fails #Putting this at the t...l cause the script to exit if any commands return a non-zero exit code....# keep track of the last executed command trap 'last_command=$current_...1534 days ago
Installing docker for Bioinformatics on Ubuntu !
.../Downloads$ docker Usage: docker [OPTIONS] COMMAND A self-sufficient runtime...nt version information and quit Management Commands: builder Manage build...ker COMMAND --help' for more information on a command.1527 days ago
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