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Problems Installing Fastphase

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
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updated by Biostar Biostar • written by mary mary

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

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written by Sukhi Singh Sukhi Singh

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

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written by Dan D Dan D

its in tar.gz format

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written by mary mary

2 answers

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

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written by Sukhi Singh Sukhi Singh

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.

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written by mary mary

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..

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written by Sukhi Singh Sukhi Singh

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.

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written by mary mary

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