Blast For Cygwin?
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12.1 years ago
Dejian ★ 1.3k

Which version of BLAST is prepared for Cygwin?

I tried to compile ncbi-blast-2.2.26+-src.tar.gz under Cygwin 1.7.13. The compilation stopped at "checking python" at first. After python was installed, the compilation stopped at "checking python2.4" after "checking python2.3". I failed to finish the compilation.

When I run "uname -a", I got "CYGWIN_NT-5.1 acer 1.7.13(0.260/5/3) 2012-04-05 12:43 i686 Cygwin". I think that ncbi-blast-2.2.26+-3.i686.rpm (159MB) was prepared for Cygwin (there is a command rpm under Cygwin). Is that right? Has anyone succeed in installing BLAST under Cygwin? (The bandwidth of my network is a bit narrow, so I want to make sure it works before downloading.)

blast • 5.6k views
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why not use the windows ones (.exe)? .rpm is the redhat installer extension (kinda like .msi for windows) you will need to install something into cygwin that can read it. have you installed the latest python?

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I have many scripts written for linux envirionment. To make them work smoothly on my laptop, cygwin is a good choice. The windows version of BLAST does not work well with cygwin, because it cannot interpret the linux-style path. I have installed python 2.6.7. Not the latest for python, but the latest under Cygwin. If the rpm version can work under cygwin after installing something necessary, that is a good news. I am trying to build a local platform similar to linux, taking the advantage of both linux and windows.

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I've had luck with virtualbox + mint running on top of windows. there seems to be some complications of getting rpm working in cygwin: http://www.redhat.com/archives/rpm-list/2000-December/msg00188.html

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11.8 years ago
Hamish ★ 3.2k

The NCBI BLAST and NCBI BLAST+ binaries provided by NCBI are not suitable for use with Cygwin. So you have three choices:

  1. Use the MS Windows binaries. If using these from a Cygwin environment you'll have to remember to use MS Windows file paths, since these binaries don't under stand UNIX paths. On the other hand if your using them from a Command Prompt or Powershell, then they behave as expected.

  2. Use the Linux binaries in Linux hosted in a virtual machine. If you are going to be doing stuff that requires a UNIX or UNIX-like environment, using a Linux distribution in a virtual machine is likely to involve significantly less effort. Using a distribution which includes NCBI BLAST, for example Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux/), or a distribution with bioinformatics packages available, for example Ubuntu (http://www.ubuntu.com/) with Debian Med (http://www.debian.org/devel/debian-med/), makes this much easier.

  3. Compile NCBI BLAST or NCBI BLAST+ from source using Cygwin. The NCBI BLAST and NCBI BLAST+ sources can be built using Cygwin and this is documented in the documentation for:

  4. The NCBI C++ Toolkit: http://www.ncbi.nlm.nih.gov/books/NBK7160/
  5. The NCBI C Toolkit: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML

Also see http://www.biostars.org/post/show/17504/blast-on-windows/

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