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Date: Tue, 10 Apr 2012 13:48:06 +0800
From: De-Jian Zhao <dejian DOT zhao AT gmail DOT com>
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To: "cygwin AT cygwin DOT com" <cygwin AT cygwin DOT com>
CC: "Buchbinder, Barry (NIH/NIAID) [E]" <BBuchbinder AT niaid DOT nih DOT gov>
Subject: Re: Can RPM packages be installed into Cygwin?
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On 2012-4-10 8:30, Buchbinder, Barry (NIH/NIAID) [E] wrote:
> De-Jian Zhao sent the following at Monday, April 09, 2012 11:12 AM
>>> On 4/8/2012 5:10 AM, De-Jian Zhao wrote:
>>>> On 2012-4-7 16:12, marco atzeri wrote:
>>>> Thanks, Marco. I was not trying to run a native linux apps, and instead
>>>> tried to rebuild the app from source. The BLAST software provides the
>>>> Build.sh and Check.sh scripts under the directory of
>>>> ncbi-blast-2.2.26+-src.tar\ncbi-blast-2.2.26+-src\c++\compilers\cygwin\.
>>>> So I think it is possible to run the software under cygwin. However, the
>>>> compilation stopped at "checking for python", even if python was
>>>> installed. That's to say, I installed the latest python and the
>>>> compilation could find it, but the compilation tried to search for
>>>> python2.3 and 2.4 further, and stopped when searching for 2.4.
>>>>
>>>> What I am concern is that whether the i686.rpm indicates it is prepared
>>>> for cygwin. As you know, when you run "uname -smo", you can get
>>>> something like this "CYGWIN_NT-5.1 i686 Cygwin". I think the package
>>>> ncbi-blast-2.2.26+-3.i686.rpm is for Cygwin. Is that right? Has anyone
>>>> ever succeeded in installing a RPM package into cygwin using "rpm -i
>>>> *rpm"?
>>>>
>>> i686.rpm is not the source package, is the binary for linux on 686
>>> processor.
>>> On cygwin we do not use rpm for building packages so the source rpm
>>> file will unlikely work.
>>>
>>> The source for all platforms is
>>>
>>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.26+-src.tar.gz
>>>
>> On 2012-4-8 14:47, marco atzeri wrote: Thank you, Marco. I tried that
>> version. Unfortunately, the compilation always stopped at "checking
>> python" even after python was installed. It seems to me that it is a
>> tough work to rebuild a software from the source code under Cygwin. The
>> dependency is hard to satisfy.
>>
>> I am curious about the utility rpm under Cygwin environment. When
>> running the setup.exe, I noticed that there is a rpm package. (Search for
>> "rpm" at the stage of "Select Packages" when running setup.exe, you can
>> find the package under "Utils Default".) Then what is it for?
> Looking at the blast directory, they have a source rpm.  Perhaps some source
> code is only available as an rpm?
>
> For what it is worth, I tried compiling and it seemed to compile OK when I
> used "./configure --without-boost" (recommended by make after a simple
> "./configure".  "make check" passed two of three tests.  YMMV.  As I did not
> install any dependencies, maybe you could do better.
>
> Also, I noted that ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
> contains some windows binaries.  You might consider using them as native
> binaries usually run faster than cygwin binaries.
>
> Also, note that there is a folder ncbi-blast-2.2.26+-src/c++/compilers/cygwin.
> I didn't notice it until after I tried compiling.  You might try to figure out
> whether the scripts there help you compile blast.
>
> IMPORTANT: I'm not a programmer, I don't work at NCBI, I have no experience in
> bioinformatics and have certainly never used BLAST.  DO NOT assume that I know
> anything about this more than what I reported above.  I was intrigued and did
> an experiment - that is all.
>
> Good luck.
>
> - Barry
>    Disclaimer: Statements made herein are not made on behalf of NIAID.
>    Disclaimer: Statements made herein are not made on behalf of NCBI.
>    Disclaimer: Statements made herein are not made on behalf of NLM.
>    Disclaimer: Statements made herein are not made on behalf of NIH.
>    Disclaimer: Statements made herein are not made on behalf of PHS.
>    Disclaimer: Statements made herein are not made on behalf of DHHS.
>

Thank you, Barry. I tried the file c++/compilers/cygwin/build.sh but 
failed. I wrote to the help desk of NCBI Blast+. They have no guidelines 
for Cygwin users and also suggested the windows version. Actually, I am 
using the windows version now. The only shortcoming is that the windows 
binaries do not recognize the linux-like Cygwin path, so the soft links 
to the blast databases become invalid. I have to change to the directory 
of the Blast database every time I want to run blast search. Anyway, it 
works although a bit inconvenient. Thanks again for your help.

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