Blat utils Linux 64-bit binaries
Ivan Adzhubey
Recent updates broke OS compatibility for Blat pre-compiled 64-bit Linux
executables once again on many our systems. Checking the dynamically linked
libraries shows:
$ ldd blat
linux-vdso.so.1 => (0x00007fffbfbc2000)
libkrb5.so.3 => /lib64/libkrb5.so.3 (0x0000003be4e00000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x000000310b400000)
libz.so.1 => /lib64/libz.so.1 (0x000000310b000000)
libm.so.6 => /lib64/libm.so.6 (0x0000003bd7e00000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003bd8600000)
libc.so.6 => /lib64/libc.so.6 (0x0000003bd7a00000)
libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x0000003be4a00000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003bd8200000)
libcom_err.so.2 => /lib64/libcom_err.so.2 (0x0000003be3a00000)
libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x0000003be4600000)
libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x0000003be5200000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x0000003bd9a00000)
/lib64/ld-linux-x86-64.so.2 (0x0000003bd7600000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x0000003bd9200000)
IMHO, that's a bit of an overkill, especially with all that libkrb5,
libk5crypto, etc stuff. Considering the security/crypto libraries are very
recent versions, the binaries simply won't run on most of the current Linux
systems (let alone ancient Linux clusters, which are in fact typical targets).
Previous iteration of the binaries, built after my similar complaint (from
10/24/2013), looked much more reasonable:
$ ldd blat
linux-vdso.so.1 => (0x00007fff683ff000)
libz.so.1 => /lib64/libz.so.1 (0x000000310b000000)
libm.so.6 => /lib64/libm.so.6 (0x0000003bd7e00000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003bd8600000)
libc.so.6 => /lib64/libc.so.6 (0x0000003bd7a00000)
/lib64/ld-linux-x86-64.so.2 (0x0000003bd7600000)
Is there any chance we might once again get something closer to the above list
instead of a more drastic "link them all and let God sort them out" approach?
Thanks,
Ivan
--
Ivan Adzhubey, Ph.D.
Instructor
Division of Genetics, Dept of Medicine
Brigham & Women's Hospital
Harvard Medical School
New Research Building, Room 0464C
77 Avenue Louis Pasteur
Boston, MA 02115
tel.: (617) 525-4728
fax: (617) 525-4705
web: http://genetics.bwh.harvard.edu/genetics/members/Ivan_Adzhubey.html
Jonathan Casper
Hello Ivan,
Thank you for your question about obtaining BLAT binaries with fewer dynamically linked libraries. Our engineers tell me that they will see what they can do about reducing the number of these dependencies. Ideally we'd like to remove as many as we possibly can, but I do not have a timetable for when an upgraded version will be ready.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
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Oscar Conchillo Solé
If you are still interested I compiled last blat version in a Rocks Cluster 5.4 (CentOS 5) I have tested it in another CentOS 5 and apparently it works in both systems (but it does not work in a Fedora12), If you want you can download it from here:
http://bioinf.uab.es/ocs/BLAT/bin/x86_64/
(Can I do that? Can I place blat executable in an open access web directory? If I can't please tell me and I'll remove it)
I hope this helps
OCS
Oscar Conchillo Solé Group of Computational Biology and Proteomics IBB Data Center Manager and Linux Sysadmin Institut de Biotecnologia I Biomedicina (UAB) mail: tx...@bioinf.uab.es telf: 0034 93581 4431; 0034 93586 8939
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Steve Heitner
Hello, Oscar.
It is fine to put the blat executable in an open access web directory, but we do ask that you please also include a license statement as seen at the top of http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/ and that you mention that the link I just referenced is the site of the official blat download.
Please contact us again at gen...@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Steve Heitner
UCSC Genome Bioinformatics Group
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