Bash commandline to install Anaconda !
...724b67d9b5f98a926ed49b834a6bb73a Anaconda3-2019.03-Linux-x86_64.sh $ bash Anaconda3-2019.03-Linux-x86_6...3/etc/profile.d/conda.csh modified /data/sata_data/workshop/wsu29/.bashrc ==> For changes to take...1555 days ago
Bash command to install Miniconda !
...s/xontrib/conda.xsh no change /data/sata_data/workshop/wsu29/miniconda3/etc/profile.d/conda.csh modified /data/sata_data/workshop/wsu29/.bashrc ==> For changes to take...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
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
Install conda on remote server !
...o/archive/Anaconda3-vers.num-Linux-x86_64.sh $ bash Anaconda3-version.num-Linux-x...m.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh $ bash Anaconda3-5.0.1-Linux-x86_64....uum.io/archive/Anaconda3-4.2.0-Linux-x86_64.sh bash Anaconda3-4.2.0-Linux-x86_64....1520 days ago
Exit Bash Script When Any Command Fails
...---------- # exit when any command fails #Putting this at the top of a bash script will cause the script...executed command trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG # echo an err...1520 days ago
Commands to install conda in Ubuntu !
...a3-2019.03-Linux-x86_64.sh jit@jit-HP-Pro-3335-MT:~/Downloads/jittmp$ bash Anaconda3-2019.03-Linux-x86_6.../home/jit/anaconda3/etc/profile.d/conda.csh modified /home/jit/.bashrc ==> For changes to take...1511 days ago
1506 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.gz1365 days ago