Skip to content

Latest commit

 

History

History
139 lines (81 loc) · 3.53 KB

general.linux.commands.md

File metadata and controls

139 lines (81 loc) · 3.53 KB

###General Linux Commands

Login command

ssh -l msze compute01 -X

Upload file

scp file.txt msze@compute01:/home/msze/data/

Upload file to second server

scp -r Hogg_Run505 msze@compute01:/home/msze/data/

Download file

scp msze@compute01:/home/msze/data/file.txt

Adding a new PATH to commands (Has to be in parent directory to set it up)

PATH=$PATH:/home/msze/data/bowtie2/bowtie2-2.1.0/bowtie2-build/:home/msze/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:; export PATH

Link (Soft) command/program with bin folder allows PATH function to search bin for command and not have to retype PATH every login

ln -s /home/msze/data/bowtie2-build /home/msze/bin/bowtie2-build

List number of files of a specific type

ls -lR *.fna | wc -l

List only specific files in a directory

ls -R | grep .pbs$

list of file and directory sizes to a text file

du -hs * | sort -h > diskusage.txt

**View Bash profile (view bash proifle file to view customizations)

nano .bash_profile

Server/computer info

*cat /proc/cpuinfo *free *cat /proc/meminfo

Short commands

*pwd -> print working directory *cd -> change directory *du -h -> directory size *rm -r -> remove a directory *rm -> remove a file *cat -> combine two files (cat file1 file2 > new.file) *ls -> list (combined with -s and -h to get file size as well) *mkdir -> make a new directory *chmod u+x XXXXX.sh -> make a shell file (use ./XXXXXXX to run) ./XXXXXXX

Axiom commands

*qsub -> submit a job *qstat -> get current jobs (combine with -u and username to be more specific) *qdel -> delete a job (use job number)

Unzip commands

*unzip -j filename.zip *tar zxvf fileNameHere.tgz *gzip -d file.gz *gunzip file.gz *bzip2 -d filename.bz2

Download commands

*Download to server using wget and ftp

wget -r -np - k ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP056/SRP056364/

definitions: - r (recursive) - np (don't follow links to parent directories) - k (to make links in downloaded HTML or CSS point to local files)

Other option definitions - nd (no directories) - e robots.off (ignore robot.txt files, dont download robots.txt files) -A png,jpg (accept only files with the extensions png or jpg) -m (mirror) (-r --timestamping --level inf --no-remove-listing)

This will download all files So you can search and download by project Using NCBI database as a reference website ftp://ftp-trace.ncbi.nih.gov metadata might be found at http://www.ncbi.nlm.nih.gov/Traces/study/

*Dowloading from MG-RAST and making a gzip file

curl http://api.metagenomics.an1.gov/1/download/mgmXXXXXX.3?file=XXX.X > mgmXXXXX.3/gz

Downloading from Dropbox

  1. Find a directory or file you want and select "share"
  2. From here select the "create link" option and copy it
  3. EXTRA NOTE:
    • Need to make sure to change the end of the link from dl=0 to dl=1

  • Download single file using a username and password (to be asked - best to use this interactively)

    • wget --max-redirect=20 --user marcasze@gmail.com --ask-password https://www.dropbox.com/s/rb35a072x3b079r/1.TCA.454Reads.fna?dl=1

  • Download using a username and password a whole directory (zipped)

    • wget -O weir.zip marcasze@gmail.com --ask-password https://www.dropbox.com/sh/d35oug6b2k7blcx/AACSx4aPKIF1RCbB3r1koqwSa?dl=1

  • Download a whole directory without using a username and passwork (zipped)

    • wget -O weir.zip https://www.dropbox.com/sh/d35oug6b2k7blcx/AACSx4aPKIF1RCbB3r1koqwSa?dl=1

Convert SRA to specific file type

*fastq-dump XXXXXXX.sra *sff-dump XXXXXXXX.sra