Installation Of Tophat-1.2.0.Linux-X86_64

Question

[07Sjdj]

i am a newcomer in bioinformatics. I am confused about the installation of tophat-1.2.0.Linux-x86_64, can someone tell me the detail procedure for it?

Thanks a lot.

[brentp]

Have a look at this thread.

Answer 1

[Giovanni M Dall'Olio]

What have you tried so far?

The x86 binaries will only work on a 64 bit machine with a 64 operating system. If that is not the case, have a look at the other discussions on tophat here in biostar to know how to do it.

The x86.64 tar file contains binary files, which means that you can use them just by calling them, without having to install them. Just decompress the file in a folder, enter it from the terminal, and type something like:

 $: cd Downloads/tophat-1.2.0.Linux_x86_64/
 $: ls
AUTHORS       closure_juncs         COPYING        fix_map_ordering  juncs_db       long_spanning_reads  prep_reads  sam_juncs      sra_to_solid  tophat_reports
bed_to_juncs  contig_to_chr_coords  extract_reads  gtf_juncs         library_stats  mask_sam             README      segment_juncs  tophat        wiggles
 $: ./long_spanning
long_spanning_reads v1.2.0 (1752)
--------------------------------------------
Usage:   long_spanning_reads <reads.fa/.fq> <possible_juncs1,...,possible_juncsN> <possible_insertions1,...,possible_insertionsN> <possible_deletions1,...,possible_deletionsN> <seg1.bwtout,...,segN.bwtout> [spliced_seg1.bwtout,...,spliced_segN.bwtout]

To include these files in your PATH and avoid having to enter the directory you have copied them every time, you can just edit your PATH variable (you are most certainly using the bash shell and you need to edit the bash variable).

As always, it is easier to get help from an online community if you explain what you have attempted first, and where exactly are you encountering difficulty.

[07Sjdj]

thanks for your help.maybe i need to learn something about the software installation in Linux operating system.

[martinkara7]

Hello, Can i ask about boost and samtools. It says on tophat web site to install but do i need to if doing by tophat-1.2.0.Linux_x86_64?

[martinkara7]

sorry me again, for linux 64bit tophat binaries file, did you have to do configure and make ... all that stuff? or just can work away?

[Giovanni M Dall'Olio]

which operating system do you have? In Ubuntu, you can just type sudo apt-get install tophat

[martinkara7]

Thanks, got it.