Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ curl -O https...b834a6bb73a Anaconda3-2019.03-Linux-x86_64.sh $ bash Anaconda3-2019.03-Linux-x86_6....csh modified /data/sata_data/workshop/wsu29/.bashrc...1566 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...iconda3/etc/profile.d/conda.csh modified /data/sata_data/workshop/wsu29/.bashrc...1566 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 che...1565 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 ## environment...1565 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.html1533 days ago
Install conda on remote server !
Please take a look at the Anaconda repo archive page https://repo.contin...Anaconda3-vers.num-Linux-x86_64.sh $ bash Anaconda3-version.num-Linux-x...ve/Anaconda3-5.0.1-Linux-x86_64.sh $ bash Anaconda3-5.0.1-Linux-x86_64....hive/Anaconda3-4.2.0-Linux-x86_64.sh bash Anac...1531 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...en any command fails #Putting this at the top of a bash script will cause the script...ap 'last_command=$current_command; current_command=$BASH_COMM...1531 days ago
Commands to install conda in Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ mkdir jittmp jit@jit-HP-Pro-3335-MT:~/Downloads$...64.sh jit@jit-HP-Pro-3335-MT:~/Downloads/jittmp$ bash Anaconda3-2019.03-Linux-x86_6...3/etc/profile.d/conda.csh modified /home/jit/.bashrc...1521 days ago
1517 days ago
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1376 days ago