Local galaxy installation problem. Please help.
Hi I am a developer for a group. I am having a problem with local installation of galaxy. The platform I am using is: $ uname -o GNU/Linux $ uname -i x86_64 $ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008 $ uname -r 2.6.9-78.0.1.ELsmp Here’s what I did: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist grep: http://www.bx.psu.edu/hg/galaxy: No such file or directory grep: galaxy_dist: No such file or directory I cut and pasted from your wiki page, and I assume there is no typo... $ tar xzf galaxy-dist-tip.tar.gz gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now $ gunzip galaxy-dist-tip.tar.gz gunzip: galaxy-dist-tip.tar.gz: unexpected end of file I guess there is something wrong with this gzipped tar file... $ rm galaxy-dist-tip.tar.gz $ /bin/rm -rf galaxy-dist Try it with bz2 file... $ bunzip2 galaxy-dist-tip.tar.bz2 $ tar xf galaxy-dist-tip.tar $ echo $? 0 $ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError: /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_64-ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader $ echo $? 1 So, I am lost now. Can somebody please give me a tip as to how to proceed? Many thanks. Regards, Tena Sakai tsakai@gallo.ucsf.edu
Tena Sakai wrote:
Hi
I am a developer for a group. I am having a problem with local installation of galaxy. The platform I am using is: $ uname -o GNU/Linux
$ uname -i x86_64
$ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008
$ uname -r 2.6.9-78.0.1.ELsmp
Here’s what I did:
$ hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist grep: http://www.bx.psu.edu/hg/galaxy: No such file or directory grep: galaxy_dist: No such file or directory
Is your 'hg' aliased to something? I am not sure why it appears to be calling grep. Also, that repository URL is out of date, I thought we'd updated it. It should still work, but the URL for the actual repository is: https://bitbucket.org/galaxy/galaxy-dist/ This has been updated in the wiki.
I cut and pasted from your wiki page, and I assume there is no typo...
$ tar xzf galaxy-dist-tip.tar.gz gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now
$ gunzip galaxy-dist-tip.tar.gz gunzip: galaxy-dist-tip.tar.gz: unexpected end of file
I guess there is something wrong with this gzipped tar file...
$ rm galaxy-dist-tip.tar.gz $ /bin/rm -rf galaxy-dist
It looks like you're right. I've contacted bitbucket and removed this link from our wiki.
Try it with bz2 file...
$ bunzip2 galaxy-dist-tip.tar.bz2 $ tar xf galaxy-dist-tip.tar $ echo $? 0
$ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError: /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_64-ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader
$ echo $? 1
So, I am lost now. Can somebody please give me a tip as to how to proceed?
I'll dig in to this last bit and get back to you ASAP.
Many thanks.
Regards,
Tena Sakai tsakai@gallo.ucsf.edu
_______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Nate Coraor wrote:
$ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008
$ uname -r 2.6.9-78.0.1.ELsmp
RHEL 4, I believe?
$ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError: /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_64-ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader
$ echo $? 1
So, I am lost now. Can somebody please give me a tip as to how to proceed?
I'll dig in to this last bit and get back to you ASAP.
It would appear that your zlib does not contain deflateSetHeader, which was added to zlib in version 1.2.2.1, released in 2004. RHEL 4.X apparently ships with zlib 1.2.1.2. If you have a newer zlib installed somewhere, you can work around this problem by setting $LD_LIBRARY_PATH to point to the directory with the newer libz.so.1. LD_LIBRARY_PATH is a hack so this is not ideal, but you may not want to override libz globally by changing something like /etc/ld.so.conf. --nate
Hi Nate, Thank you for your reply. I am getting there, but I need a bit more help. Firstly, yes, I had an alias hg (which was "history | grep $1"). I got rid of it and hg is working fine. Secondly, I installed the latest version of zlib (1.2.5) and I can go further with "sh run.sh", but it hangs after it tells me: File "/usr/local/lib/python2.5/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: (98, 'Address already in use') When I point my browser to http://vixen:8080 (vixen is the very machine on which I am implementing galaxy), a tomcat page comes up (telling me that tomcat is running fine). Here's my question: Is there a way to run galaxy on ports other than 8080? Thank you! Regards, Tena Sakai PS: Thank you for updating the link on wiki page. On 2/17/11 9:57 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Nate Coraor wrote:
$ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008
$ uname -r 2.6.9-78.0.1.ELsmp
RHEL 4, I believe?
$ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError: /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_64 -ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader
$ echo $? 1
So, I am lost now. Can somebody please give me a tip as to how to proceed?
I'll dig in to this last bit and get back to you ASAP.
It would appear that your zlib does not contain deflateSetHeader, which was added to zlib in version 1.2.2.1, released in 2004. RHEL 4.X apparently ships with zlib 1.2.1.2. If you have a newer zlib installed somewhere, you can work around this problem by setting $LD_LIBRARY_PATH to point to the directory with the newer libz.so.1. LD_LIBRARY_PATH is a hack so this is not ideal, but you may not want to override libz globally by changing something like /etc/ld.so.conf.
--nate
Tena Sakai wrote:
Hi Nate,
Thank you for your reply.
I am getting there, but I need a bit more help.
Firstly, yes, I had an alias hg (which was "history | grep $1"). I got rid of it and hg is working fine.
Secondly, I installed the latest version of zlib (1.2.5) and I can go further with "sh run.sh", but it hangs after it tells me: File "/usr/local/lib/python2.5/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: (98, 'Address already in use')
When I point my browser to http://vixen:8080 (vixen is the very machine on which I am implementing galaxy), a tomcat page comes up (telling me that tomcat is running fine).
Here's my question: Is there a way to run galaxy on ports other than 8080?
Yes, in the file universe_wsgi.ini in the root of the Galaxy directory, one of the options near the top of the file is 'port ='. This can be changed to whatever you prefer. --nate
Thank you!
Regards,
Tena Sakai
PS: Thank you for updating the link on wiki page.
On 2/17/11 9:57 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Nate Coraor wrote:
$ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008
$ uname -r 2.6.9-78.0.1.ELsmp
RHEL 4, I believe?
$ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError: /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_64 -ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader
$ echo $? 1
So, I am lost now. Can somebody please give me a tip as to how to proceed?
I'll dig in to this last bit and get back to you ASAP.
It would appear that your zlib does not contain deflateSetHeader, which was added to zlib in version 1.2.2.1, released in 2004. RHEL 4.X apparently ships with zlib 1.2.1.2. If you have a newer zlib installed somewhere, you can work around this problem by setting $LD_LIBRARY_PATH to point to the directory with the newer libz.so.1. LD_LIBRARY_PATH is a hack so this is not ideal, but you may not want to override libz globally by changing something like /etc/ld.so.conf.
--nate
Hi Nate, I am still not there, though I am getting closer... I changed the port to 8888 in universe_wsgi.ini and Here's what appears on my screen: galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,285 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,287 Enabling 'x-forwarded-host' middleware Starting server in PID 28721. serving on http://127.0.0.1:8888 When I try to go there on my browser, the complaint from browser (I used both safari and firefox) is: Firefox can't establish a connection to the server at vixen:8888. Or Safari can¹t open the page ³http://vixen:8888/² because Safari can¹t connect to the server ³vixen². But when I change 8888 to 8080, I do get a page from tomcat. I see that the process is running: $ ps axl | grep 28721 0 1026 28721 28588 15 0 390520 83456 finish Tl pts/9 0:14 python ./scripts/paster.py serve universe_wsgi.ini 0 1026 28781 27316 16 0 51116 668 pipe_w S+ pts/9 0:00 grep 28721 Any clue, why I can't get there by browser? Thank you. Regards, Tena Sakai On 2/17/11 12:57 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Tena Sakai wrote:
Hi Nate,
Thank you for your reply.
I am getting there, but I need a bit more help.
Firstly, yes, I had an alias hg (which was "history | grep $1"). I got rid of it and hg is working fine.
Secondly, I installed the latest version of zlib (1.2.5) and I can go further with "sh run.sh", but it hangs after it tells me: File "/usr/local/lib/python2.5/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: (98, 'Address already in use')
When I point my browser to http://vixen:8080 (vixen is the very machine on which I am implementing galaxy), a tomcat page comes up (telling me that tomcat is running fine).
Here's my question: Is there a way to run galaxy on ports other than 8080?
Yes, in the file universe_wsgi.ini in the root of the Galaxy directory, one of the options near the top of the file is 'port ='. This can be changed to whatever you prefer.
--nate
Thank you!
Regards,
Tena Sakai
PS: Thank you for updating the link on wiki page.
On 2/17/11 9:57 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Nate Coraor wrote:
$ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008
$ uname -r 2.6.9-78.0.1.ELsmp
RHEL 4, I believe?
$ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError: /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_ 64 -ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader
$ echo $? 1
So, I am lost now. Can somebody please give me a tip as to how to proceed?
I'll dig in to this last bit and get back to you ASAP.
It would appear that your zlib does not contain deflateSetHeader, which was added to zlib in version 1.2.2.1, released in 2004. RHEL 4.X apparently ships with zlib 1.2.1.2. If you have a newer zlib installed somewhere, you can work around this problem by setting $LD_LIBRARY_PATH to point to the directory with the newer libz.so.1. LD_LIBRARY_PATH is a hack so this is not ideal, but you may not want to override libz globally by changing something like /etc/ld.so.conf.
--nate
The output:
Starting server in PID 28721. serving on http://127.0.0.1:8888
means that you have configured Galaxy to ONLY listen for connections from the server (localhost) itself so it will refuse connections from other machines. If you change 127.0.0.1 to 0.0.0.0 in universe_wsgi.ini and restart Galaxy, it will accept connections from other machines. One more complication - this will ONLY work if port 8888 is open for incoming connections - the server is likely to have a firewall that blocks any incoming connections as servers are typically configured to refuse connections other than on well known ports so you may need to adjust the server's firewall. On Fri, Feb 18, 2011 at 8:48 AM, Tena Sakai <tsakai@gallo.ucsf.edu> wrote:
Hi Nate,
I am still not there, though I am getting closer...
I changed the port to 8888 in universe_wsgi.ini and Here's what appears on my screen: galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,285 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,287 Enabling 'x-forwarded-host' middleware Starting server in PID 28721. serving on http://127.0.0.1:8888
When I try to go there on my browser, the complaint from browser (I used both safari and firefox) is: Firefox can't establish a connection to the server at vixen:8888. Or Safari can¹t open the page ³http://vixen:8888/² because Safari can¹t connect to the server ³vixen². But when I change 8888 to 8080, I do get a page from tomcat.
I see that the process is running: $ ps axl | grep 28721 0 1026 28721 28588 15 0 390520 83456 finish Tl pts/9 0:14 python ./scripts/paster.py serve universe_wsgi.ini 0 1026 28781 27316 16 0 51116 668 pipe_w S+ pts/9 0:00 grep 28721
Any clue, why I can't get there by browser?
Thank you.
Regards,
Tena Sakai
On 2/17/11 12:57 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Tena Sakai wrote:
Hi Nate,
Thank you for your reply.
I am getting there, but I need a bit more help.
Firstly, yes, I had an alias hg (which was "history | grep $1"). I got rid of it and hg is working fine.
Secondly, I installed the latest version of zlib (1.2.5) and I can go further with "sh run.sh", but it hangs after it tells me: File "/usr/local/lib/python2.5/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: (98, 'Address already in use')
When I point my browser to http://vixen:8080 (vixen is the very machine on which I am implementing galaxy), a tomcat page comes up (telling me that tomcat is running fine).
Here's my question: Is there a way to run galaxy on ports other than 8080?
Yes, in the file universe_wsgi.ini in the root of the Galaxy directory, one of the options near the top of the file is 'port ='. This can be changed to whatever you prefer.
--nate
Thank you!
Regards,
Tena Sakai
PS: Thank you for updating the link on wiki page.
On 2/17/11 9:57 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Nate Coraor wrote:
$ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008
$ uname -r 2.6.9-78.0.1.ELsmp
RHEL 4, I believe?
$ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError: /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_ 64 -ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader
$ echo $? 1
So, I am lost now. Can somebody please give me a tip as to how to proceed?
I'll dig in to this last bit and get back to you ASAP.
It would appear that your zlib does not contain deflateSetHeader, which was added to zlib in version 1.2.2.1, released in 2004. RHEL 4.X apparently ships with zlib 1.2.1.2. If you have a newer zlib installed somewhere, you can work around this problem by setting $LD_LIBRARY_PATH to point to the directory with the newer libz.so.1. LD_LIBRARY_PATH is a hack so this is not ideal, but you may not want to override libz globally by changing something like /etc/ld.so.conf.
--nate
_______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Ross Lazarus MBBS MPH Associate Professor, HMS; Director of Bioinformatics, Channing Laboratory; 181 Longwood Ave., Boston MA 02115, USA. Tel: +1 617 505 4850 Head, Medical Bioinformatics, BakerIDI; PO Box 6492, St Kilda Rd Central; Melbourne, VIC 8008, Australia; Tel: +61 385321444
Hi Nate, Please ignore my previous post. I got it working. I changed an entry in universe_wsgi.ini file.
From "#host = 127.0.0.1" to "host = vixen.egcrc.org". It appears to be working.
Many thanks for your help. Regards, Tena Sakai On 2/17/11 1:48 PM, "Tena Sakai" <tsakai@gallo.ucsf.edu> wrote:
Hi Nate,
I am still not there, though I am getting closer...
I changed the port to 8888 in universe_wsgi.ini and Here's what appears on my screen: galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,285 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,287 Enabling 'x-forwarded-host' middleware Starting server in PID 28721. serving on http://127.0.0.1:8888
When I try to go there on my browser, the complaint from browser (I used both safari and firefox) is: Firefox can't establish a connection to the server at vixen:8888. Or Safari can¹t open the page ³http://vixen:8888/² because Safari can¹t connect to the server ³vixen². But when I change 8888 to 8080, I do get a page from tomcat.
I see that the process is running: $ ps axl | grep 28721 0 1026 28721 28588 15 0 390520 83456 finish Tl pts/9 0:14 python ./scripts/paster.py serve universe_wsgi.ini 0 1026 28781 27316 16 0 51116 668 pipe_w S+ pts/9 0:00 grep 28721
Any clue, why I can't get there by browser?
Thank you.
Regards,
Tena Sakai
On 2/17/11 12:57 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Tena Sakai wrote:
Hi Nate,
Thank you for your reply.
I am getting there, but I need a bit more help.
Firstly, yes, I had an alias hg (which was "history | grep $1"). I got rid of it and hg is working fine.
Secondly, I installed the latest version of zlib (1.2.5) and I can go further with "sh run.sh", but it hangs after it tells me: File "/usr/local/lib/python2.5/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: (98, 'Address already in use')
When I point my browser to http://vixen:8080 (vixen is the very machine on which I am implementing galaxy), a tomcat page comes up (telling me that tomcat is running fine).
Here's my question: Is there a way to run galaxy on ports other than 8080?
Yes, in the file universe_wsgi.ini in the root of the Galaxy directory, one of the options near the top of the file is 'port ='. This can be changed to whatever you prefer.
--nate
Thank you!
Regards,
Tena Sakai
PS: Thank you for updating the link on wiki page.
On 2/17/11 9:57 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Nate Coraor wrote:
$ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008
$ uname -r 2.6.9-78.0.1.ELsmp
RHEL 4, I believe?
$ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError:
/home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86>>>>>> _
64 -ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader
$ echo $? 1
So, I am lost now. Can somebody please give me a tip as to how to proceed?
I'll dig in to this last bit and get back to you ASAP.
It would appear that your zlib does not contain deflateSetHeader, which was added to zlib in version 1.2.2.1, released in 2004. RHEL 4.X apparently ships with zlib 1.2.1.2. If you have a newer zlib installed somewhere, you can work around this problem by setting $LD_LIBRARY_PATH to point to the directory with the newer libz.so.1. LD_LIBRARY_PATH is a hack so this is not ideal, but you may not want to override libz globally by changing something like /etc/ld.so.conf.
--nate
_______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Tena Sakai wrote:
Hi Nate,
I am still not there, though I am getting closer...
I changed the port to 8888 in universe_wsgi.ini and Here's what appears on my screen: galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,285 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,287 Enabling 'x-forwarded-host' middleware Starting server in PID 28721. serving on http://127.0.0.1:8888
When I try to go there on my browser, the complaint from browser (I used both safari and firefox) is: Firefox can't establish a connection to the server at vixen:8888. Or Safari can¹t open the page ³http://vixen:8888/² because Safari can¹t connect to the server ³vixen².
See the 'host =' line in universe_wsgi.ini. To listen on the network (instead of just localhost), change the value to: host = 0.0.0.0 --nate
But when I change 8888 to 8080, I do get a page from tomcat.
I see that the process is running: $ ps axl | grep 28721 0 1026 28721 28588 15 0 390520 83456 finish Tl pts/9 0:14 python ./scripts/paster.py serve universe_wsgi.ini 0 1026 28781 27316 16 0 51116 668 pipe_w S+ pts/9 0:00 grep 28721
Any clue, why I can't get there by browser?
Thank you.
Regards,
Tena Sakai
On 2/17/11 12:57 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Tena Sakai wrote:
Hi Nate,
Thank you for your reply.
I am getting there, but I need a bit more help.
Firstly, yes, I had an alias hg (which was "history | grep $1"). I got rid of it and hg is working fine.
Secondly, I installed the latest version of zlib (1.2.5) and I can go further with "sh run.sh", but it hangs after it tells me: File "/usr/local/lib/python2.5/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: (98, 'Address already in use')
When I point my browser to http://vixen:8080 (vixen is the very machine on which I am implementing galaxy), a tomcat page comes up (telling me that tomcat is running fine).
Here's my question: Is there a way to run galaxy on ports other than 8080?
Yes, in the file universe_wsgi.ini in the root of the Galaxy directory, one of the options near the top of the file is 'port ='. This can be changed to whatever you prefer.
--nate
Thank you!
Regards,
Tena Sakai
PS: Thank you for updating the link on wiki page.
On 2/17/11 9:57 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Nate Coraor wrote:
$ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008
$ uname -r 2.6.9-78.0.1.ELsmp
RHEL 4, I believe?
$ cd galaxy-dist $ sh run.sh <...lots of lines here...> Fetch successful. <...more lines here...> ysam/csamtools.py", line 6, in __bootstrap__ ImportError: /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_ 64 -ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader
$ echo $? 1
So, I am lost now. Can somebody please give me a tip as to how to proceed?
I'll dig in to this last bit and get back to you ASAP.
It would appear that your zlib does not contain deflateSetHeader, which was added to zlib in version 1.2.2.1, released in 2004. RHEL 4.X apparently ships with zlib 1.2.1.2. If you have a newer zlib installed somewhere, you can work around this problem by setting $LD_LIBRARY_PATH to point to the directory with the newer libz.so.1. LD_LIBRARY_PATH is a hack so this is not ideal, but you may not want to override libz globally by changing something like /etc/ld.so.conf.
--nate
participants (3)
-
Nate Coraor -
Ross -
Tena Sakai