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RE: Can RPM packages be installed into Cygwin?
- 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?
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
>>> 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
>> i686.rpm is not the source package, is the binary for linux on 686
>> On cygwin we do not use rpm for building packages so the source rpm
>> file will unlikely work.
>> The source for all platforms is
>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.
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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