Question: Problems Installing Fastphase
0
gravatar for mary
7.1 years ago by
mary210
Bologna university
mary210 wrote:

Dear all,

I try to reconstruct haplotype by fastphase in my data, i download it from http://stephenslab.uchicago.edu/software.html for ubuntu 12.10. but I think it has problem, because when I want to unzip by command as gunzip and tar -zxvf its didn't recognize a tar format. is there any body that try for downloading fastphase and use it on ubuntu for test it. I used it at 6 month ago but now it dose not work. I am tired to try several time for download and extract it , but it didn't work. the phase do haplotype reconstruction can i used phase instead of fastphase?

thanks a lot

haplotype • 4.7k views
ADD COMMENTlink modified 5.7 years ago by Biostar ♦♦ 20 • written 7.1 years ago by mary210
1

Please edit the title to something useful, like "Problem installing fastPhase". Also, the link u've mentioned, a login is required.

ADD REPLYlink written 7.1 years ago by Sukhdeep Singh9.9k

What is the extension of the file you downloaded? For example: .gz, .tar.gz, .zip

ADD REPLYlink written 7.1 years ago by Dan D6.9k

its in tar.gz format

ADD REPLYlink written 7.0 years ago by mary210
0
gravatar for Sukhdeep Singh
7.0 years ago by
Sukhdeep Singh9.9k
Netherlands
Sukhdeep Singh9.9k wrote:

It should be recognizable by tar, if its a tarball. Did you check the manual,

2.1 Installation

Presumably, you have downloaded a fastphase.VERSION.linux.tar.gz file. (Alternatively, you downloaded an executable file for Solaris, Darwin 1 , or for Microsoft Windows 2 .) Then do the following:

gunzip fastphase.VERSION.linux.tar.gz
tar -xvf fastphase.VERSION.linux.tar

This will produce a folder similar in name to fastphase.VERSION.linux. Contained in this new directory are the following:

• fastPHASE

• fastphase.inp an example input file

• fastphase haplotypes.inp an example input file of known haplotypes

• fastphase subpoplabels.inp file of “subpopulation” labels for individuals in fastphase.inp

• fastphase subpoplabels2.inp contains enough labels to run with -b -ufastphase subpoplabels2.inp flags.

To do a short run and test that the program is working on your system:

./fastPHASE -T1

I cannot help more, because I am not able to download the software without a licence.

Cheers

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by Sukhdeep Singh9.9k
0
gravatar for mary
7.0 years ago by
mary210
Bologna university
mary210 wrote:

ok , i write what i did 1- I went to: http://depts.washington.edu/fphase/download/ 2- I downloaded fastPHASELinux32bit.gz 3- i did gunzip fastPHASELinux32bit.gz , because i didn't found gz.tar format . in instruction write" do gunzip file and after tar -xvf file" but the file is in gz format. after i did gunzip its didnt make a folder with above file, it just make fastPHASE.exe . and ./fastPHASE -T1 didn't work this software is free and you can register and install it.

ADD COMMENTlink written 7.0 years ago by mary210

1) please add it as an comment.

2) you again sent the same url' which requires id and password.

3) I cannot help without looking at the file.

4) It doesn't makes sense to me, why source code labelled as fastPHASELinux32bit.gz, will give you an .exe file , which is a windows based installer. You can try, wine fastPHASE.exe and see what happens..

ADD REPLYlink modified 7.0 years ago • written 7.0 years ago by Sukhdeep Singh9.9k

rthe problem is that , it give me fastphase.exe, anyway, please see this link: http://c4c.uwc4c.com/express_license_technologies/fastphase in this web page in academic section you can click to license. in Licensee info, you can register. then they send for you a link that you can connect to download the software and use it.

ADD REPLYlink written 7.0 years ago by mary210
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