Linux Software Installation - Cornell University

Linux Software Installation

Part 1

Qi Sun Bioinformatics Facility

Components of software E.g. gzip

$which gzip /usr/bin/gzip

Main executable

$ldd /usr/bin/gzip

linux-vdso.so.1 => (0x00007ffd46732000) libc.so.6 => /lib64/libc.so.6 (0x00007fd7cb256l0Sib0hr0aar)reieds /lib64/ld-linux-x86-64.so.2 (0x00007fd7cb623000)

Where are the files?

/usr/

/usr/local/

bin lib lib64 bin lib lib64

Software come with the system. E.g. "ls"

Extra software installed by administrator

BioHPC administrators install software in /programs/

/home/$USER

Software installed by yourself

When running a software ? 1. executable

The system find the executable file through $PATH

Default $PATH in BioHPC

$echo $PATH /programs/docker/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/programs/bin/mummer:/programs/bin/util: /programs/bin/bowtie:/programs/bin/bwa:/programs/bin/cufflinks:/programs/bin/samtools:/programs/bin/tophat:/ programs/bin/fastx:/programs/bin/blast:/programs/bin/igv:/programs/bin/velvet:/programs/bin/iAssembler:/progra ms/bin/GATK:/programs/bin/454:/programs/bin/blat:/programs/bin/perlscripts..................

Add path to the $PATH variable

export PATH=/home/xxxxx/bin:$PATH

Use "which" command to find the executable file:

which bwa /programs/bin/bwa/bwa

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