From: "Buchbinder, Barry (NIH/NIAID) [E]" <BBuchbinder AT niaid DOT nih DOT gov>
To: "cygwin AT cygwin DOT com" <cygwin AT cygwin DOT com>
CC: "'De-Jian Zhao'" <dejian DOT zhao AT gmail DOT com>,
        marco atzeri	<marco DOT atzeri AT gmail DOT com>
Date: Mon, 9 Apr 2012 20:30:41 -0400
Subject: RE: Can RPM packages be installed into Cygwin?
Message-ID: <0105D5C1E0353146B1B222348B0411A20A6559C3C2@NIHMLBX02.nih.gov>
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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.

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