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Lancer plusieurs commandes successives#

cmd1 ; cmd2 → cmd2 exécutée une fois la cmd1 finie
cmd1 && cmd2 → cmd2 exécutée uniquement si cmd1 correctement finie

Example

`wget linux.tar.gz && tar -zxvf linux.tar.gz`

Lancer un processus en “arrière plan”#

  • cmd1 & Lancer un processus en arrière plan
  • jobs Connaître les processus qui tournent en arrière-plan
  • fg <job_number> Récupérer un processus au premier plan
  • bg <job_number> Envoyer un processus en arrière plan
  • nohup cmd1 & “Détacher” le processus de la console. Fonctionne même quand la console est fermée, si deconnexion
  • Ctrl + Z Stopper un processus

Practice 3 : Using the && separator#

  • On the console, type the 2 following linux commands to get data necessary for the next :
# get the file on the web and decompress the gzip file 
wget http://itrop.ird.fr/LINUX-TP/LINUX4JEDI-TP.tar.gz && tar -xzvf LINUX4JEDI-TP.tar.gz
  • Check the content of your home directory on the server now
  • Delete the file LINUX4JEDI.tar.gz on the server - rm
  • Execute the tree command
details 
bash-4.2# tree -L 2  
.
|-- 1-fastq
|   |-- SRR8517015_1.10000.fastq
|   |-- SRR8517015_2.10000.fastq
|   |-- SRX5320622_1.10000.fastq
|   |-- SRX5320622_2.10000.fastq
|   |-- SRX5320631_1.10000.fastq
|   `-- SRX5320631_2.10000.fastq
|-- 2-bam
|   |-- B1.starMSU7.chr1.sorted.bam
|   |-- B1.starMSU7.chr1.sorted.bam.bai
|   |-- B2.starMSU7.chr1.sorted.bam
|   |-- B2.starMSU7.chr1.sorted.bam.bai
|   |-- G1.starMSU7.chr1.sorted.bam
|   |-- G1.starMSU7.chr1.sorted.bam.bai
|   |-- G2.starMSU7.chr1.sorted.bam
|   `-- G2.starMSU7.chr1.sorted.bam.bai
|-- 3-RNAseqCount
|   |-- erz340_suppl_supplementary_table_s5.csv
|   `-- erz340_suppl_supplementary_table_s5_new.csv
|-- 4-vcf
|   `-- OgOb-all-MSU7-CHR6.GATKVARIANTFILTRATION.shuf.100000.vcf.gz
|-- 9-denovoAssembly
|   |-- DAOSW_abyss-contigs.fa -> Ob/DAOSW_abyss-contigs.fa
|   |-- Ob
|   |-- Og
|   `-- TOG5681_abyss-contigs.fa -> Og/TOG5681_abyss-contigs.fa
|-- Bank
|   |-- all.con
|   `-- all.seq
|-- Other
|   |-- abcd.txt
|   |-- contact.txt
|   |-- example.txt
|   `-- test.list
|-- Script
|   |-- helloworld-var.sh
|   |-- helloworld.sh
|   |-- q
|   |-- script.sh
|   `-- testNum.sh
|-- erz340.pdf
`-- erz340_suppl_supplementary_table_s1.csv