I download the latest version of tabix (tabix-0.2.6.tar.bz2.1) and decompress the software with command tar xjvf. Even I used "bgzip" command without any option or with -help option inside the folder, the error information -bash: bgzip: command not found still showed up. Is something wrong with the command that I used for decompressing the software?
I list here of the files in the folder where tabix-0.2.6.tar.bz2.1 was decompressed for your reference. Please help me out with this! Thank you very much in advance!
-rw-r----- 1 chenglin Users 1064 Jun 18 2012 bam_endian.h
-rw-r----- 1 chenglin Users 3774 Jun 18 2012 bedidx.c
-rw-r----- 1 chenglin Users 17067 Jun 18 2012 bgzf.c
-rw-r----- 1 chenglin Users 5744 Jun 18 2012 bgzf.h
-rw-r----- 1 chenglin Users 5903 Jun 18 2012 bgzip.c
-rw-r----- 1 chenglin Users 19196 Jun 18 2012 ChangeLog
-rw-r----- 1 chenglin Users 3778 Jun 18 2012 example.gtf.gz
-rw-r----- 1 chenglin Users 259 Jun 18 2012 example.gtf.gz.tbi
-rw-r----- 1 chenglin Users 26641 Jun 18 2012 index.c
-rw-r----- 1 chenglin Users 16522 Jun 18 2012 khash.h
-rw-r----- 1 chenglin Users 18281 Jun 18 2012 knetfile.c
-rw-r----- 1 chenglin Users 1611 Jun 18 2012 knetfile.h
-rw-r----- 1 chenglin Users 8108 Jun 18 2012 kseq.h
-rw-r----- 1 chenglin Users 9672 Jun 18 2012 ksort.h
-rw-r----- 1 chenglin Users 4009 Jun 18 2012 kstring.c
-rw-r----- 1 chenglin Users 1587 Jun 18 2012 kstring.h
-rw-r----- 1 chenglin Users 11813 Jun 18 2012 main.c
-rw-r----- 1 chenglin Users 1527 Jun 18 2012 Makefile
-rw-r----- 1 chenglin Users 2789 Jun 18 2012 NEWS
drwxr-x--- 3 chenglin Users 4096 Jun 18 2012 perl
drwxr-x--- 2 chenglin Users 4096 Jun 18 2012 python
-rw-r----- 1 chenglin Users 3862 Jun 18 2012 tabix.1
-rw-r----- 1 chenglin Users 4712 Jun 18 2012 tabix.h
-rwxr-x--- 1 chenglin Users 3027 Jun 18 2012 tabix.py
-rw-r----- 1 chenglin Users 12042 Jun 18 2012 TabixReader.java
-rw-r----- 1 chenglin Users 4876 Jun 18 2012 tabix.tex
1 answer
what you've downloaded is the source code. you have to compile it before being able to use it. type make in that folder uncompressed folder, and you should end up with a tabix binary in it.
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Problem with using tabix
written by Chenglin
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Indels.vcf and SNPs.vcf from GATK ftp.
written by always_learning
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Is Casava Multithreaded?
written by Misha •
Hello chenglin.ch!
I realise this was a problem with a piece of bioinformatics software, but the resolution is basic command line use, so it is off-topic for the site. You may find http://superuser.com/ more useful
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
Thank you for your suggestion! No problem.
Cheers!
chenglin