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Re: Can RPM packages be installed into Cygwin?
- From: De-Jian Zhao <dejian dot zhao at gmail dot com>
- To: "cygwin at cygwin dot com" <cygwin at cygwin dot com>
- Cc: "Buchbinder, Barry (NIH/NIAID) [E]" <BBuchbinder at niaid dot nih dot gov>
- Date: Tue, 10 Apr 2012 13:48:06 +0800
- Subject: Re: Can RPM packages be installed into Cygwin?
- References: <0105D5C1E0353146B1B222348B0411A20A6559C3C2@NIHMLBX02.nih.gov>
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
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.
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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