At a very wild guess
-bash-samtools
This looks shaky. For a start you need a space between the command and the application in all Linux/Unix/Mac OS X applications (its complicated to explain right now [see below] just accept it).
Wait you are using sudo
and thats how you are installing on a local machine. sudo
on a remote machine will never work, because you are not the systems admin. sudo
on a local machine is not cool (see below)
Anyway I need to do some next-gen and have 6 MiSeq kits waiting for action so I installed it from here:
http://www.htslib.org/download/
Okay so here's my tcsh history
4 21:44 cd sam* # like I was in the Desktop
7 21:44 more README # I needed to know how they wanted the installation
8 21:45 ./configure # okay there are setting the paths for me - saves me a job
11 21:46 make # like fairytale stuff for a load of C scripts
16 21:49 ls | grep samtools # I wanna know if its compiled and I see samtools* ... yep
17 21:49 ln -s ./samtools* ~/bin # I'm gonna pop a link in my bin so after I type
18 21:49 rehash # 'cause I still insist on tcsh rather than bash (don't do it in bash)
However, the following is a bit creepy because I get loads of perl scripts in my /usr/local/bin ...
make install
Anyway,
samtools
It took 4 mins on an OS X machine, using tsch, after I just quaffed 2 pints at my pub (10pm London time). So probability is set against me ....
OUTPUT
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.18 (r982:295)
Usage: samtools <command> [options]
Command: view SAM<->BAM conversion
sort sort alignment file
mpileup multi-way pileup
depth compute the depth
faidx index/extract FASTA
tview text alignment viewer
index index alignment
idxstats BAM index stats (r595 or later)
etc ...
BTW seriously, fun over, avoid "sudo
" if you can, for lots of reasons (which I'm not gonna explain). Its a last resort and usually means your paths are incorrectly set.
sudo will be refused on a remote machine, without question. You COULD ask systems admin to do this for you. HOWEVER, I'd try and install yourself without sudo
and your bioinformatics will benefit.
Program: samtools (Tools for alignments in the SAM format)
Version: 1.9 (using htslib 1.9)
Usage: samtools <command> [options]
Commands:
-- Indexing
dict create a sequence dictionary file
faidx index/extract FASTA
fqidx index/extract FASTQ
index index alignment
Output following make install