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. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
