not sure what I can do about this...
Hello Gents, So someone asked me to install the package Prokka on Galaxy. I did and everything went well! However, the following error comes up, when they try to work with Prokka: Fatal error: Exit code 2 () [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. [20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z outdir\/prokka\.err -i outdir\/prokka\.fsa 2> /dev/null According to a google search, there is very little on this error. And it has been around for a while but I didn't find a posted solution. Any suggestions? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218
Hi Edgar, please download the latest version of tbl2asn from here: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/ and replace it with your version, this will probably fix your error. Cheers, Bjoern Am 29.09.2015 um 14:05 schrieb Fernandez Edgar:
Hello Gents,
So someone asked me to install the package Prokka on Galaxy. I did and everything went well!
However, the following error comes up, when they try to work with Prokka:
Fatal error: Exit code 2 ()
[tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version.
[20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z outdir\/prokka\.err -i outdir\/prokka\.fsa 2> /dev/null
According to a google search, there is very little on this error. And it has been around for a while but I didn't find a posted solution.
Any suggestions?
Cordialement / Regards,
Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568
Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hello Björn, Thank you for answering! When I installed Prokka from the Galaxy ToolShed, all the dependencies were installed too. tbl2asn is one of those dependencies... How would I replace it? Cordialement / Regards, Edgar Fernandez -----Message d'origine----- De : Björn Grüning [mailto:bjoern.gruening@gmail.com] Envoyé : September-29-15 8:10 AM À : Fernandez Edgar; galaxy-dev@bx.psu.edu Objet : Re: [galaxy-dev] not sure what I can do about this... Hi Edgar, please download the latest version of tbl2asn from here: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/ and replace it with your version, this will probably fix your error. Cheers, Bjoern Am 29.09.2015 um 14:05 schrieb Fernandez Edgar:
Hello Gents,
So someone asked me to install the package Prokka on Galaxy. I did and everything went well!
However, the following error comes up, when they try to work with Prokka:
Fatal error: Exit code 2 ()
[tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version.
[20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z outdir\/prokka\.err -i outdir\/prokka\.fsa 2> /dev/null
According to a google search, there is very little on this error. And it has been around for a while but I didn't find a posted solution.
Any suggestions?
Cordialement / Regards,
Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568
Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hello Björn,
Thank you for answering! When I installed Prokka from the Galaxy ToolShed, all the dependencies were installed too. tbl2asn is one of those dependencies... How would I replace it?
Cordialement / Regards, Edgar Fernandez
The way the NCBI deliberately make tbl2asn expire is very annoying for packaging and breaks strict reproducibility :( I think Bjoern was suggesting manually updating the copy of tbl2asn which the Tool Shed had downloaded (as a quick short term solution). You'd need to find this file within the Tool Shed dependencies folder... Philip - can you update package_tbl2asn_23_7 or add a new package if the version number has changed? Or would you like the IUC group to look after this in future? https://toolshed.g2.bx.psu.edu/view/takadonet/package_tbl2asn_23_7/ Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4? https://toolshed.g2.bx.psu.edu/view/crs4/prokka/ Peter
I will make a new package for tbl2asn. Our lab is not too happy that tbl2asn expires and causes lots of issues for us. On Tue, Sep 29, 2015 at 9:24 AM Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hello Björn,
Thank you for answering! When I installed Prokka from the Galaxy ToolShed, all the dependencies were installed too. tbl2asn is one of those dependencies... How would I replace it?
Cordialement / Regards, Edgar Fernandez
The way the NCBI deliberately make tbl2asn expire is very annoying for packaging and breaks strict reproducibility :(
I think Bjoern was suggesting manually updating the copy of tbl2asn which the Tool Shed had downloaded (as a quick short term solution). You'd need to find this file within the Tool Shed dependencies folder...
Philip - can you update package_tbl2asn_23_7 or add a new package if the version number has changed? Or would you like the IUC group to look after this in future?
https://toolshed.g2.bx.psu.edu/view/takadonet/package_tbl2asn_23_7/
Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4?
https://toolshed.g2.bx.psu.edu/view/crs4/prokka/
Peter
Guys, I can express how thankful I am for your help!!! Personally, I would comment out the following line in the tbl2asn code: 8869<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8869> if (MoreThanYearOld<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=MoreThanYearOld> ()) { 8870<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8870> too_old = TRUE<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=TRUE>; 8871<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8871> Message<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=Message> (MSG_POST<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=MSG_POST>, "This copy of tbl2asn is more than a year old. Please download the current version."); 8872<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8872> } In the meantime, would you suggest I change the files located inside my galaxy installation? Or should I wait for Philip’s release? I ask because I found the following binary files: -rwxr-x--- 1 galaxy users 7349340 Sep 15 08:52 ./tool-data/toolshed.dependency.dir/tbl2asn/23.7/takadonet/package_tbl2asn_23_7/2271d52a8531/bin/tbl2asn -rwxrwxr-x 1 galaxy users 12675348 Jul 28 2014 ./tool-data/toolshed.dependency.dir/prokka/1.10/crs4/prokka/3ad7ef0ba385/binaries/darwin/tbl2asn -rwxrwxr-x 1 galaxy users 6872896 Jul 28 2014 ./tool-data/toolshed.dependency.dir/prokka/1.10/crs4/prokka/3ad7ef0ba385/binaries/linux/tbl2asn Oddly, they’re all different. What exactly can I do with this and how can I compile the tblasn.c file? Cordialement / Regards, Edgar Fernandez De : Philip Mabon [mailto:philipmabon@gmail.com] Envoyé : September-29-15 10:27 AM À : Peter Cock; Fernandez Edgar; Nicola Soranzo (TGAC) Cc : Björn Grüning; galaxy-dev@bx.psu.edu Objet : Re: [galaxy-dev] not sure what I can do about this... I will make a new package for tbl2asn. Our lab is not too happy that tbl2asn expires and causes lots of issues for us. On Tue, Sep 29, 2015 at 9:24 AM Peter Cock <p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>> wrote: On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca<mailto:edgar.fernandez@umontreal.ca>> wrote:
Hello Björn,
Thank you for answering! When I installed Prokka from the Galaxy ToolShed, all the dependencies were installed too. tbl2asn is one of those dependencies... How would I replace it?
Cordialement / Regards, Edgar Fernandez
The way the NCBI deliberately make tbl2asn expire is very annoying for packaging and breaks strict reproducibility :( I think Bjoern was suggesting manually updating the copy of tbl2asn which the Tool Shed had downloaded (as a quick short term solution). You'd need to find this file within the Tool Shed dependencies folder... Philip - can you update package_tbl2asn_23_7 or add a new package if the version number has changed? Or would you like the IUC group to look after this in future? https://toolshed.g2.bx.psu.edu/view/takadonet/package_tbl2asn_23_7/ Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4? https://toolshed.g2.bx.psu.edu/view/crs4/prokka/ Peter
Hi Fernandez, 2015-09-29 10:02 GMT-05:00 Fernandez Edgar <edgar.fernandez@umontreal.ca>:
Guys, I can express how thankful I am for your help!!!
Personally, I would comment out the following line in the tbl2asn code:
8869 <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8869> if (MoreThanYearOld <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=MoreThanYearOld> ()) {
8870 <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8870> too_old = TRUE <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=TRUE>;
8871 <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8871> Message <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=Message> ( MSG_POST <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=MSG_POST>, *"This copy of tbl2asn is more than a year old. **Please download the current version."*);
8872 <http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8872> }
In the meantime, would you suggest I change the files located inside my galaxy installation?
Or should I wait for Philip’s release?
I would replace the files. We (The IUC, specifically Björn and myself) have talked about solutions to this problem but haven't finished building them yet.
I ask because I found the following binary files:
-rwxr-x--- 1 galaxy users 7349340 Sep 15 08:52
./tool-data/toolshed.dependency.dir/tbl2asn/23.7/takadonet/package_tbl2asn_23_7/2271d52a8531/bin/tbl2asn
-rwxrwxr-x 1 galaxy users 12675348 Jul 28 2014
./tool-data/toolshed.dependency.dir/prokka/1.10/crs4/prokka/3ad7ef0ba385/binaries/darwin/tbl2asn
-rwxrwxr-x 1 galaxy users 6872896 Jul 28 2014
./tool-data/toolshed.dependency.dir/prokka/1.10/crs4/prokka/3ad7ef0ba385/binaries/linux/tbl2asn
Oddly, they’re all different.
What exactly can I do with this and how can I compile the tblasn.c file?
You can fetch a precompiled version of tbl2asn here: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/ I recommend replacing all of those (or just the first and last, assuming you're on linux) as (eventually) none of them will work. Hopefully in the future we'll be able to fix this.
Cordialement / Regards,
Edgar Fernandez
*De :* Philip Mabon [mailto:philipmabon@gmail.com] *Envoyé :* September-29-15 10:27 AM *À :* Peter Cock; Fernandez Edgar; Nicola Soranzo (TGAC) *Cc :* Björn Grüning; galaxy-dev@bx.psu.edu *Objet :* Re: [galaxy-dev] not sure what I can do about this...
I will make a new package for tbl2asn. Our lab is not too happy that tbl2asn expires and causes lots of issues for us.
On Tue, Sep 29, 2015 at 9:24 AM Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hello Björn,
Thank you for answering! When I installed Prokka from the Galaxy ToolShed, all the dependencies were installed too. tbl2asn is one of those dependencies... How would I replace it?
Cordialement / Regards, Edgar Fernandez
The way the NCBI deliberately make tbl2asn expire is very annoying for packaging and breaks strict reproducibility :(
I think Bjoern was suggesting manually updating the copy of tbl2asn which the Tool Shed had downloaded (as a quick short term solution). You'd need to find this file within the Tool Shed dependencies folder...
Philip - can you update package_tbl2asn_23_7 or add a new package if the version number has changed? Or would you like the IUC group to look after this in future?
https://toolshed.g2.bx.psu.edu/view/takadonet/package_tbl2asn_23_7/
Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4?
https://toolshed.g2.bx.psu.edu/view/crs4/prokka/
Peter
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
On 29/09/15 15:24, Peter Cock wrote:
Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4?
https://toolshed.g2.bx.psu.edu/view/crs4/prokka/
Peter
I can update prokka, no problem. Just let me know when the new package_tbl2asn is available. Cheers, Nicola
Just waiting on this merge request and I will have a new version on the toolshed. https://github.com/bgruening/download_store/pull/5 On Tue, Sep 29, 2015 at 1:25 PM Nicola Soranzo <nsoranzo@tiscali.it> wrote:
On 29/09/15 15:24, Peter Cock wrote:
Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4?
https://toolshed.g2.bx.psu.edu/view/crs4/prokka/
Peter
I can update prokka, no problem. Just let me know when the new package_tbl2asn is available.
Cheers, Nicola
Repo is done and works correctly. https://toolshed.g2.bx.psu.edu/repository?repository_id=862266fc8a7cd60b&changeset_revision=41764d6a6a3c Cheers On Tue, Sep 29, 2015 at 1:47 PM Philip Mabon <philipmabon@gmail.com> wrote:
Just waiting on this merge request and I will have a new version on the toolshed.
https://github.com/bgruening/download_store/pull/5
On Tue, Sep 29, 2015 at 1:25 PM Nicola Soranzo <nsoranzo@tiscali.it> wrote:
On 29/09/15 15:24, Peter Cock wrote:
Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4?
https://toolshed.g2.bx.psu.edu/view/crs4/prokka/
Peter
I can update prokka, no problem. Just let me know when the new package_tbl2asn is available.
Cheers, Nicola
Thanks Philip, I've updated the prokka package accordingly and I have also updated other dependencies (Prokka 1.11, Barrnap 0.7, BLAST 2.2.31, HMMER 3.1b2). Edgar, I'd like to know if the new version installs and works for you, since I'm not using it at the moment. Cheers, Nicola On 30/09/15 14:30, Philip Mabon wrote:
Repo is done and works correctly.
Cheers
On Tue, Sep 29, 2015 at 1:47 PM Philip Mabon <philipmabon@gmail.com <mailto:philipmabon@gmail.com>> wrote:
Just waiting on this merge request and I will have a new version on the toolshed.
https://github.com/bgruening/download_store/pull/5
On Tue, Sep 29, 2015 at 1:25 PM Nicola Soranzo <nsoranzo@tiscali.it <mailto:nsoranzo@tiscali.it>> wrote:
On 29/09/15 15:24, Peter Cock wrote: > Nicola - once that's done, can you update the prokka dependency > list - or would that fall to your old colleagues at CRS4? > > https://toolshed.g2.bx.psu.edu/view/crs4/prokka/ > > Peter
I can update prokka, no problem. Just let me know when the new package_tbl2asn is available.
Cheers, Nicola
I will give it a try today or tomorrow. Thanks On Thu, Oct 1, 2015 at 1:21 PM Nicola Soranzo <nsoranzo@tiscali.it> wrote:
Thanks Philip, I've updated the prokka package accordingly and I have also updated other dependencies (Prokka 1.11, Barrnap 0.7, BLAST 2.2.31, HMMER 3.1b2).
Edgar, I'd like to know if the new version installs and works for you, since I'm not using it at the moment.
Cheers, Nicola
On 30/09/15 14:30, Philip Mabon wrote:
Repo is done and works correctly.
Cheers
On Tue, Sep 29, 2015 at 1:47 PM Philip Mabon <philipmabon@gmail.com> wrote:
Just waiting on this merge request and I will have a new version on the toolshed.
https://github.com/bgruening/download_store/pull/5
On Tue, Sep 29, 2015 at 1:25 PM Nicola Soranzo <nsoranzo@tiscali.it> wrote:
On 29/09/15 15:24, Peter Cock wrote:
Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4?
https://toolshed.g2.bx.psu.edu/view/crs4/prokka/
Peter
I can update prokka, no problem. Just let me know when the new package_tbl2asn is available.
Cheers, Nicola
Hey Guys, Hope everyone is doing well. So I’m back at galaxy v16.01 I’m having a small problem. My python system version is 2.6.6 So I installed python version 2.7.8 from Software Collection Library release 1.2 packages for Oracle Linux 6 (x86_64)<https://ulns.dit.umontreal.ca/rhn/channels/ChannelDetail.do?cid=149> This means I need to source an environment before being about to use it. So what I’ve created a file config/local_env.sh with: # Source python27 export PATH=/opt/rh/python27/root/usr/bin${PATH:+:${PATH}} export LD_LIBRARY_PATH=/opt/rh/python27/root/usr/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}} export MANPATH=/opt/rh/python27/root/usr/share/man:${MANPATH} # For systemtap export XDG_DATA_DIRS=/opt/rh/python27/root/usr/share${XDG_DATA_DIRS:+:${XDG_DATA_DIRS}} # For pkg-config export PKG_CONFIG_PATH=/opt/rh/python27/root/usr/lib64/pkgconfig${PKG_CONFIG_PATH:+:${PKG_CONFIG_PATH}} These export comes directly with the installation of python 2.7.8 in the file /opt/rh/python27/enable. But when I started my galaxy it didn’t stick. I had to insert those exports into the file run.sh right before the following line: ./scripts/common_startup.sh $common_startup_args || exit 1 Any suggestions to make it work? Also, I get this error : Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1061, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 223, in run result = self.command() File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 639, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 295, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 319, in loadobj global_conf=global_conf) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext global_conf=global_conf) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 368, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 506, in get_context section) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 565, in _context_from_explicit value = import_string(found_expr) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/home/galaxy/galaxy-v16.01/lib/galaxy/web/buildapp.py", line 5, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module> import galaxy.app File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in <module> from galaxy import config, jobs File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in <module> from galaxy import model, util File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in <module> import galaxy.datatypes.registry File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, in <module> import tabular File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, in <module> from galaxy.datatypes.sniff import get_headers File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in <module> from galaxy.datatypes.binary import Binary File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in <module> import pysam File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module> from pysam.libchtslib import * ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64 Removing PID file paster.pid PLEASE HELP ME ! Best regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568
Hey Guys, I’ve fixed my first problem with the environment. But I’m still getting the second one. Also, did any of you guys try to deploy galaxy with Microsoft Azure? I’m actually looking into it and I was wondering if you had any input… Let me know if you have any info on my libchtslib.so: input error or Microsoft Azure. Cheers! Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568 From: Fernandez Edgar Sent: May-18-16 2:00 PM To: galaxy-dev@bx.psu.edu Subject: RE: [galaxy-dev] not sure what I can do about this... Hey Guys, Hope everyone is doing well. So I’m back at galaxy v16.01 I’m having a small problem. My python system version is 2.6.6 So I installed python version 2.7.8 from Software Collection Library release 1.2 packages for Oracle Linux 6 (x86_64)<https://ulns.dit.umontreal.ca/rhn/channels/ChannelDetail.do?cid=149> This means I need to source an environment before being about to use it. So what I’ve created a file config/local_env.sh with: # Source python27 export PATH=/opt/rh/python27/root/usr/bin${PATH:+:${PATH}} export LD_LIBRARY_PATH=/opt/rh/python27/root/usr/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}} export MANPATH=/opt/rh/python27/root/usr/share/man:${MANPATH} # For systemtap export XDG_DATA_DIRS=/opt/rh/python27/root/usr/share${XDG_DATA_DIRS:+:${XDG_DATA_DIRS}} # For pkg-config export PKG_CONFIG_PATH=/opt/rh/python27/root/usr/lib64/pkgconfig${PKG_CONFIG_PATH:+:${PKG_CONFIG_PATH}} These export comes directly with the installation of python 2.7.8 in the file /opt/rh/python27/enable. But when I started my galaxy it didn’t stick. I had to insert those exports into the file run.sh right before the following line: ./scripts/common_startup.sh $common_startup_args || exit 1 Any suggestions to make it work? Also, I get this error : Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1061, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 223, in run result = self.command() File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 639, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 295, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 319, in loadobj global_conf=global_conf) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext global_conf=global_conf) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 368, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 506, in get_context section) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 565, in _context_from_explicit value = import_string(found_expr) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/home/galaxy/galaxy-v16.01/lib/galaxy/web/buildapp.py", line 5, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module> import galaxy.app File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in <module> from galaxy import config, jobs File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in <module> from galaxy import model, util File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in <module> import galaxy.datatypes.registry File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, in <module> import tabular File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, in <module> from galaxy.datatypes.sniff import get_headers File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in <module> from galaxy.datatypes.binary import Binary File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in <module> import pysam File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module> from pysam.libchtslib import * ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64 Removing PID file paster.pid PLEASE HELP ME ! Best regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568
Hi Edgar, it’s a good idea to use python2.7 for galaxy, since 16.01 is the last release supporting python 2.6. In general you can create a new virrtualenv with a a specific python interpreter like this: virtualenv -p <path/to/python/interpreter> <path/to/new/virtualenv/> If you create a new new virtualenv .venv in your galaxy source folder, run.sh will pick this up. If you are using a different way to start galaxy, you can use something along the lines of <path/to/virtualenv/bin/python <path/to/galaxy>/scripts/paster.py serve <path/to/galaxy/>config/galaxy.ini> Hope that will get you past the problems starting up galaxy. Cheers, Marius On 19 May 2016 at 14:48, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hey Guys,
I’ve fixed my first problem with the environment.
But I’m still getting the second one.
Also, did any of you guys try to deploy galaxy with Microsoft Azure?
I’m actually looking into it and I was wondering if you had any input…
Let me know if you have any info on my libchtslib.so: input error or Microsoft Azure.
Cheers!
*Edgar Fernandez*
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
*Université de Montréal*
PAVILLON ROGER-GAUDRY, bureau X-210
( Bur. : *1-514-343-6111 poste 16568*
*From:* Fernandez Edgar *Sent:* May-18-16 2:00 PM *To:* galaxy-dev@bx.psu.edu *Subject:* RE: [galaxy-dev] not sure what I can do about this...
Hey Guys,
Hope everyone is doing well.
So I’m back at galaxy v16.01
I’m having a small problem.
My python system version is 2.6.6
So I installed python version 2.7.8 from Software Collection Library release 1.2 packages for Oracle Linux 6 (x86_64) <https://ulns.dit.umontreal.ca/rhn/channels/ChannelDetail.do?cid=149>
This means I need to source an environment before being about to use it.
So what I’ve created a file config/local_env.sh with:
*# Source python27*
*export PATH=/opt/rh/python27/root/usr/bin${PATH:+:${PATH}}*
*export LD_LIBRARY_PATH=/opt/rh/python27/root/usr/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}*
*export MANPATH=/opt/rh/python27/root/usr/share/man:${MANPATH}*
*# For systemtap*
*export XDG_DATA_DIRS=/opt/rh/python27/root/usr/share${XDG_DATA_DIRS:+:${XDG_DATA_DIRS}}*
*# For pkg-config*
*export PKG_CONFIG_PATH=/opt/rh/python27/root/usr/lib64/pkgconfig${PKG_CONFIG_PATH:+:${PKG_CONFIG_PATH}}*
These export comes directly with the installation of python 2.7.8 in the file /opt/rh/python27/enable.
But when I started my galaxy it didn’t stick.
I had to insert those exports into the file run.sh right before the following line:
*./scripts/common_startup.sh $common_startup_args || exit 1*
Any suggestions to make it work?
Also, I get this error :
*Traceback (most recent call last):*
* File "./scripts/paster.py", line 27, in <module>*
* serve.run()*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1061, in run*
* invoke(command, command_name, options, args[1:])*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke*
* exit_code = runner.run(args)*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 223, in run*
* result = self.command()*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 639, in command*
* app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 295, in loadapp*
* return loadobj(APP, uri, name=name, **kw)*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 319, in loadobj*
* global_conf=global_conf)*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext*
* global_conf=global_conf)*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 368, in _loadconfig*
* return loader.get_context(object_type, name, global_conf)*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 506, in get_context*
* section)*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 565, in _context_from_explicit*
* value = import_string(found_expr)*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string*
* return pkg_resources.EntryPoint.parse("x=" + s).load(False)*
* File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load*
* entry = __import__(self.module_name, globals(),globals(), ['__name__'])*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/web/buildapp.py", line 5, in <module>*
* from galaxy.webapps.galaxy.buildapp import app_factory*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module>*
* import galaxy.app*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in <module>*
* from galaxy import config, jobs*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in <module>*
* from galaxy import model, util*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in <module>*
* import galaxy.datatypes.registry*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, in <module>*
* import tabular*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, in <module>*
* from galaxy.datatypes.sniff import get_headers*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in <module>*
* from galaxy.datatypes.binary import Binary*
* File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in <module>*
* import pysam*
* File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module>*
* from pysam.libchtslib import **
*ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64*
*Removing PID file paster.pid*
PLEASE HELP ME !
Best regards,
*Edgar Fernandez*
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
*Université de Montréal*
PAVILLON ROGER-GAUDRY, bureau X-210
( Bur. : *1-514-343-6111 poste 16568*
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hello guys, I’m still stuck on this error. I’ve installed a brand new galaxy v16.01 And when I start it, I get the big error mentioned below. Here’s the last message in the error: ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64 Thanks for your assistance! Cheers, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568 From: Fernandez Edgar Sent: May-19-16 8:48 AM To: 'galaxy-dev@bx.psu.edu' <galaxy-dev@bx.psu.edu> Subject: RE: [galaxy-dev] not sure what I can do about this... Hey Guys, I’ve fixed my first problem with the environment. But I’m still getting the second one. Also, did any of you guys try to deploy galaxy with Microsoft Azure? I’m actually looking into it and I was wondering if you had any input… Let me know if you have any info on my libchtslib.so: input error or Microsoft Azure. Cheers! Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568 From: Fernandez Edgar Sent: May-18-16 2:00 PM To: galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> Subject: RE: [galaxy-dev] not sure what I can do about this... Hey Guys, Hope everyone is doing well. So I’m back at galaxy v16.01 I’m having a small problem. My python system version is 2.6.6 So I installed python version 2.7.8 from Software Collection Library release 1.2 packages for Oracle Linux 6 (x86_64)<https://ulns.dit.umontreal.ca/rhn/channels/ChannelDetail.do?cid=149> This means I need to source an environment before being about to use it. So what I’ve created a file config/local_env.sh with: # Source python27 export PATH=/opt/rh/python27/root/usr/bin${PATH:+:${PATH}} export LD_LIBRARY_PATH=/opt/rh/python27/root/usr/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}} export MANPATH=/opt/rh/python27/root/usr/share/man:${MANPATH} # For systemtap export XDG_DATA_DIRS=/opt/rh/python27/root/usr/share${XDG_DATA_DIRS:+:${XDG_DATA_DIRS}} # For pkg-config export PKG_CONFIG_PATH=/opt/rh/python27/root/usr/lib64/pkgconfig${PKG_CONFIG_PATH:+:${PKG_CONFIG_PATH}} These export comes directly with the installation of python 2.7.8 in the file /opt/rh/python27/enable. But when I started my galaxy it didn’t stick. I had to insert those exports into the file run.sh right before the following line: ./scripts/common_startup.sh $common_startup_args || exit 1 Any suggestions to make it work? Also, I get this error : Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1061, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 223, in run result = self.command() File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 639, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 295, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 319, in loadobj global_conf=global_conf) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 344, in loadcontext global_conf=global_conf) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 368, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 506, in get_context section) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 565, in _context_from_explicit value = import_string(found_expr) File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/home/galaxy/galaxy-v16.01/lib/galaxy/web/buildapp.py", line 5, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module> import galaxy.app File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in <module> from galaxy import config, jobs File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in <module> from galaxy import model, util File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in <module> import galaxy.datatypes.registry File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, in <module> import tabular File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, in <module> from galaxy.datatypes.sniff import get_headers File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in <module> from galaxy.datatypes.binary import Binary File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in <module> import pysam File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module> from pysam.libchtslib import * ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64 Removing PID file paster.pid PLEASE HELP ME ! Best regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568
Hi Fernandez, We saw something very like that with mixed versions of Linux, specifically our Galaxy head node where pysam was installed had CentOS 7, but the node where Galaxy was trying to run the metadata detection was CentOS 6. Unfortunately I do not have a record of the exact traceback - but from memory it was the same problem in pysam with gzopen64. (We'd already fought problems with Python mis-matches, GLIBC versions, etc and had carefully built Python on CentOS 6 in order to run on both CentOS 6 and 7.) At this point we gave up, and will run the Galaxy node on the same version of Linux as the Cluster - and plan to upgrade the cluster before the Galaxy node. That way all the stuff Galaxy installs (e.g. via the ToolShed) ought to work on the cluster. Peter On Tue, May 24, 2016 at 7:08 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hello guys,
I’m still stuck on this error.
I’ve installed a brand new galaxy v16.01
And when I start it, I get the big error mentioned below.
Here’s the last message in the error:
ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64
Thanks for your assistance!
Cheers,
Edgar Fernandez
Hello Peter, What would your suggestion be? Wait until a new version of galaxy is compatible with my Oracle Linux 6 ? Best regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 I Bur. : 1-514-343-6111 poste 16568 -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: May-24-16 2:29 PM To: Fernandez Edgar <edgar.fernandez@umontreal.ca> Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] not sure what I can do about this... Hi Fernandez, We saw something very like that with mixed versions of Linux, specifically our Galaxy head node where pysam was installed had CentOS 7, but the node where Galaxy was trying to run the metadata detection was CentOS 6. Unfortunately I do not have a record of the exact traceback - but from memory it was the same problem in pysam with gzopen64. (We'd already fought problems with Python mis-matches, GLIBC versions, etc and had carefully built Python on CentOS 6 in order to run on both CentOS 6 and 7.) At this point we gave up, and will run the Galaxy node on the same version of Linux as the Cluster - and plan to upgrade the cluster before the Galaxy node. That way all the stuff Galaxy installs (e.g. via the ToolShed) ought to work on the cluster. Peter On Tue, May 24, 2016 at 7:08 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hello guys,
I’m still stuck on this error.
I’ve installed a brand new galaxy v16.01
And when I start it, I get the big error mentioned below.
Here’s the last message in the error:
ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/lib chtslib.so: undefined symbol: gzopen64
Thanks for your assistance!
Cheers,
Edgar Fernandez
Hi Edgar, Are your Galaxy server AND your cluster are all running Oracle Linux 6? If yes, my guess about the cluster using an older version of Linux compared to the Galaxy server is unrelated. Peter On Tue, May 24, 2016 at 7:47 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hello Peter,
What would your suggestion be? Wait until a new version of galaxy is compatible with my Oracle Linux 6 ?
Best regards,
Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210 I Bur. : 1-514-343-6111 poste 16568
Hello Peter, For now, my new installation of galaxy v16.01 is on one test desktop running Oracle Linux 6. Before changing my production installation, I'm doing my due diligent. Let me know what you think... Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 I Bur. : 1-514-343-6111 poste 16568 -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: May-24-16 5:40 PM To: Fernandez Edgar <edgar.fernandez@umontreal.ca> Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] not sure what I can do about this... Hi Edgar, Are your Galaxy server AND your cluster are all running Oracle Linux 6? If yes, my guess about the cluster using an older version of Linux compared to the Galaxy server is unrelated. Peter On Tue, May 24, 2016 at 7:47 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hello Peter,
What would your suggestion be? Wait until a new version of galaxy is compatible with my Oracle Linux 6 ?
Best regards,
Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210 I Bur. : 1-514-343-6111 poste 16568
Sorry Edgar, It looks like something else is causing this error (and my guess about different versions of Linux on Galaxy and the cluster was wrong): ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64 It may be important how the pysam wheel was compiled, perhaps Nate may be able to comment (CC'd). Peter On Wed, May 25, 2016 at 12:40 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hello Peter,
For now, my new installation of galaxy v16.01 is on one test desktop running Oracle Linux 6. Before changing my production installation, I'm doing my due diligent.
Let me know what you think...
Edgar Fernandez
Hey guys, I believe I figure it out. The problem is my Oracle Linux 6 repository slowness of updates. I have libz 1.2.3 installed and that version is missing gzopen64. However, the version 1.2.8 exists and is not out for oracle. Here is what I did to find and please pay attention to the colored code : [root@gavroche] [08:59:24] [/tmp] [39 files - 8.0Mb] [0]# ldd /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so linux-vdso.so.1 => (0x00007ffd4cfad000) libz.so.1 => /lib64/libz.so.1 (0x00007f4435cf2000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f4435ad5000) libc.so.6 => /lib64/libc.so.6 (0x00007f4435740000) /lib64/ld-linux-x86-64.so.2 (0x00000033ef400000) [root@gavroche] [08:59:29] [/tmp] [39 files - 8.0Mb] [0]# ls -al /lib64/libz.so.1 lrwxrwxrwx. 1 root root 13 Oct 22 2014 /lib64/libz.so.1 -> libz.so.1.2.3 [root@gavroche] [08:59:34] [/tmp] [39 files - 8.0Mb] [0]# ldd /lib64/libz.so.1.2.3 linux-vdso.so.1 => (0x00007ffd9dcce000) libc.so.6 => /lib64/libc.so.6 (0x00000033ef800000) /lib64/ld-linux-x86-64.so.2 (0x00000033ef400000) [root@gavroche] [09:00:02] [/tmp] [39 files - 8.0Mb] [0]# readelf -a /lib64/libz.so.1.2.3 ELF Header: Magic: 7f 45 4c 46 02 01 01 00 00 00 00 00 00 00 00 00 Class: ELF64 Data: 2's complement, little endian Version: 1 (current) OS/ABI: UNIX - System V ABI Version: 0 Type: DYN (Shared object file) Machine: Advanced Micro Devices X86-64 Version: 0x1 Entry point address: 0x33f0802120 Start of program headers: 64 (bytes into file) Start of section headers: 89112 (bytes into file) Flags: 0x0 Size of this header: 64 (bytes) Size of program headers: 56 (bytes) Number of program headers: 7 Size of section headers: 64 (bytes) Number of section headers: 31 Section header string table index: 30 Section Headers: [Nr] Name Type Address Offset Size EntSize Flags Link Info Align [ 0] NULL 0000000000000000 00000000 0000000000000000 0000000000000000 0 0 0 [ 1] .note.gnu.build-i NOTE 00000033f08001c8 000001c8 0000000000000024 0000000000000000 A 0 0 4 [ 2] .gnu.hash GNU_HASH 00000033f08001f0 000001f0 00000000000002a8 0000000000000000 A 3 0 8 [ 3] .dynsym DYNSYM 00000033f0800498 00000498 0000000000000a80 0000000000000018 A 4 2 8 [ 4] .dynstr STRTAB 00000033f0800f18 00000f18 00000000000004c6 0000000000000000 A 0 0 1 [ 5] .gnu.version VERSYM 00000033f08013de 000013de 00000000000000e0 0000000000000002 A 3 0 2 [ 6] .gnu.version_d VERDEF 00000033f08014c0 000014c0 00000000000000ec 0000000000000000 A 4 7 8 [ 7] .gnu.version_r VERNEED 00000033f08015b0 000015b0 0000000000000040 0000000000000000 A 4 1 8 [ 8] .rela.dyn RELA 00000033f08015f0 000015f0 0000000000000330 0000000000000018 A 3 0 8 [ 9] .rela.plt RELA 00000033f0801920 00001920 00000000000004b0 0000000000000018 A 3 11 8 [10] .init PROGBITS 00000033f0801dd0 00001dd0 0000000000000018 0000000000000000 AX 0 0 4 [11] .plt PROGBITS 00000033f0801de8 00001de8 0000000000000330 0000000000000010 AX 0 0 4 [12] .text PROGBITS 00000033f0802120 00002120 000000000000b288 0000000000000000 AX 0 0 16 [13] .fini PROGBITS 00000033f080d3a8 0000d3a8 000000000000000e 0000000000000000 AX 0 0 4 [14] .rodata PROGBITS 00000033f080d3c0 0000d3c0 00000000000060be 0000000000000000 A 0 0 32 [15] .eh_frame_hdr PROGBITS 00000033f0813480 00013480 00000000000002bc 0000000000000000 A 0 0 4 [16] .eh_frame PROGBITS 00000033f0813740 00013740 0000000000000d34 0000000000000000 A 0 0 8 [17] .ctors PROGBITS 00000033f0a14cd8 00014cd8 0000000000000010 0000000000000000 WA 0 0 8 [18] .dtors PROGBITS 00000033f0a14ce8 00014ce8 0000000000000010 0000000000000000 WA 0 0 8 [19] .jcr PROGBITS 00000033f0a14cf8 00014cf8 0000000000000008 0000000000000000 WA 0 0 8 [20] .data.rel.ro PROGBITS 00000033f0a14d00 00014d00 00000000000000f8 0000000000000000 WA 0 0 32 [21] .dynamic DYNAMIC 00000033f0a14df8 00014df8 00000000000001b0 0000000000000010 WA 4 0 8 [22] .got PROGBITS 00000033f0a14fa8 00014fa8 0000000000000040 0000000000000008 WA 0 0 8 [23] .got.plt PROGBITS 00000033f0a14fe8 00014fe8 00000000000001a8 0000000000000008 WA 0 0 8 [24] .data PROGBITS 00000033f0a151a0 000151a0 0000000000000060 0000000000000000 WA 0 0 32 [25] .bss NOBITS 00000033f0a15200 00015200 0000000000000010 0000000000000000 WA 0 0 8 [26] .gnu_debuglink PROGBITS 0000000000000000 00015200 0000000000000018 0000000000000000 0 0 4 [27] .gnu.liblist GNU_LIBLIST 0000000000000000 00015218 0000000000000028 0000000000000014 28 0 4 [28] .gnu.libstr STRTAB 0000000000000000 00015240 0000000000000027 0000000000000000 0 0 1 [29] .gnu.prelink_undo PROGBITS 0000000000000000 00015268 0000000000000888 0000000000000001 0 0 8 [30] .shstrtab STRTAB 0000000000000000 00015af0 0000000000000125 0000000000000000 0 0 1 Key to Flags: W (write), A (alloc), X (execute), M (merge), S (strings) I (info), L (link order), G (group), x (unknown) O (extra OS processing required) o (OS specific), p (processor specific) There are no section groups in this file. Program Headers: Type Offset VirtAddr PhysAddr FileSiz MemSiz Flags Align LOAD 0x0000000000000000 0x00000033f0800000 0x00000033f0800000 0x0000000000014474 0x0000000000014474 R E 200000 LOAD 0x0000000000014cd8 0x00000033f0a14cd8 0x00000033f0a14cd8 0x0000000000000528 0x0000000000000538 RW 200000 DYNAMIC 0x0000000000014df8 0x00000033f0a14df8 0x00000033f0a14df8 0x00000000000001b0 0x00000000000001b0 RW 8 NOTE 0x00000000000001c8 0x00000033f08001c8 0x00000033f08001c8 0x0000000000000024 0x0000000000000024 R 4 GNU_EH_FRAME 0x0000000000013480 0x00000033f0813480 0x00000033f0813480 0x00000000000002bc 0x00000000000002bc R 4 GNU_STACK 0x0000000000000000 0x0000000000000000 0x0000000000000000 0x0000000000000000 0x0000000000000000 RW 8 GNU_RELRO 0x0000000000014cd8 0x00000033f0a14cd8 0x00000033f0a14cd8 0x0000000000000328 0x0000000000000328 R 1 Section to Segment mapping: Segment Sections... 00 .note.gnu.build-id .gnu.hash .dynsym .dynstr .gnu.version .gnu.version_d .gnu.version_r .rela.dyn .rela.plt .init .plt .text .fini .rodata .eh_frame_hdr .eh_frame 01 .ctors .dtors .jcr .data.rel.ro .dynamic .got .got.plt .data .bss 02 .dynamic 03 .note.gnu.build-id 04 .eh_frame_hdr 05 06 .ctors .dtors .jcr .data.rel.ro .dynamic .got Dynamic section at offset 0x14df8 contains 25 entries: Tag Type Name/Value 0x0000000000000001 (NEEDED) Shared library: [libc.so.6] 0x000000000000000e (SONAME) Library soname: [libz.so.1] 0x000000000000000c (INIT) 0x33f0801dd0 0x000000000000000d (FINI) 0x33f080d3a8 0x000000006ffffef5 (GNU_HASH) 0x33f08001f0 0x0000000000000005 (STRTAB) 0x33f0800f18 0x0000000000000006 (SYMTAB) 0x33f0800498 0x000000000000000a (STRSZ) 1222 (bytes) 0x000000000000000b (SYMENT) 24 (bytes) 0x0000000000000003 (PLTGOT) 0x33f0a14fe8 0x0000000000000002 (PLTRELSZ) 1200 (bytes) 0x0000000000000014 (PLTREL) RELA 0x0000000000000017 (JMPREL) 0x33f0801920 0x0000000000000007 (RELA) 0x33f08015f0 0x0000000000000008 (RELASZ) 816 (bytes) 0x0000000000000009 (RELAENT) 24 (bytes) 0x000000006ffffffc (VERDEF) 0x33f08014c0 0x000000006ffffffd (VERDEFNUM) 7 0x000000006ffffffe (VERNEED) 0x33f08015b0 0x000000006fffffff (VERNEEDNUM) 1 0x000000006ffffff0 (VERSYM) 0x33f08013de 0x000000006ffffff9 (RELACOUNT) 26 0x000000006ffffdf8 (CHECKSUM) 0xb158153e 0x000000006ffffdf5 (GNU_PRELINKED) 2016-02-23T09:02:06 0x0000000000000000 (NULL) 0x0 Relocation section '.rela.dyn' at offset 0x15f0 contains 34 entries: Offset Info Type Sym. Value Sym. Name + Addend 0033f0a14d08 000000000008 R_X86_64_RELATIVE 00000033f0805940 0033f0a14d18 000000000008 R_X86_64_RELATIVE 00000033f0805540 0033f0a14d28 000000000008 R_X86_64_RELATIVE 00000033f0805540 0033f0a14d38 000000000008 R_X86_64_RELATIVE 00000033f0805540 0033f0a14d48 000000000008 R_X86_64_RELATIVE 00000033f0804ff0 0033f0a14d58 000000000008 R_X86_64_RELATIVE 00000033f0804ff0 0033f0a14d68 000000000008 R_X86_64_RELATIVE 00000033f0804ff0 0033f0a14d78 000000000008 R_X86_64_RELATIVE 00000033f0804ff0 0033f0a14d88 000000000008 R_X86_64_RELATIVE 00000033f0804ff0 0033f0a14d98 000000000008 R_X86_64_RELATIVE 00000033f0804ff0 0033f0a14da0 000000000008 R_X86_64_RELATIVE 00000033f0811eac 0033f0a14da8 000000000008 R_X86_64_RELATIVE 00000033f0811ebc 0033f0a14db0 000000000008 R_X86_64_RELATIVE 00000033f080d3c5 0033f0a14db8 000000000008 R_X86_64_RELATIVE 00000033f0811ec7 0033f0a14dc0 000000000008 R_X86_64_RELATIVE 00000033f0811ed2 0033f0a14dc8 000000000008 R_X86_64_RELATIVE 00000033f0811edf 0033f0a14dd0 000000000008 R_X86_64_RELATIVE 00000033f0811eea 0033f0a14dd8 000000000008 R_X86_64_RELATIVE 00000033f0811efe 0033f0a14de0 000000000008 R_X86_64_RELATIVE 00000033f0811f0b 0033f0a14de8 000000000008 R_X86_64_RELATIVE 00000033f080d3c5 0033f0a14df0 000000000008 R_X86_64_RELATIVE 00000033f0a14df0 0033f0a151a0 000000000008 R_X86_64_RELATIVE 00000033f0811740 0033f0a151a8 000000000008 R_X86_64_RELATIVE 00000033f0811c60 0033f0a151c0 000000000008 R_X86_64_RELATIVE 00000033f0811bc0 0033f0a151c8 000000000008 R_X86_64_RELATIVE 00000033f0811d60 0033f0a151e8 000000000008 R_X86_64_RELATIVE 00000033f0811e60 0033f0a14fa8 000500000006 R_X86_64_GLOB_DAT 0000000000000000 __gmon_start__ + 0 0033f0a14fb0 000600000006 R_X86_64_GLOB_DAT 0000000000000000 _Jv_RegisterClasses + 0 0033f0a14fb8 004d00000006 R_X86_64_GLOB_DAT 00000033f0808da0 zcalloc + 0 0033f0a14fc0 000f00000006 R_X86_64_GLOB_DAT 0000000000000000 __cxa_finalize + 0 0033f0a14fc8 005e00000006 R_X86_64_GLOB_DAT 00000033f0811640 _length_code + 0 0033f0a14fd0 003e00000006 R_X86_64_GLOB_DAT 00000033f0811440 _dist_code + 0 0033f0a14fd8 003f00000006 R_X86_64_GLOB_DAT 00000033f0a14da0 z_errmsg + 0 0033f0a14fe0 005400000006 R_X86_64_GLOB_DAT 00000033f0808d90 zcfree + 0 Relocation section '.rela.plt' at offset 0x1920 contains 50 entries: Offset Info Type Sym. Value Sym. Name + Addend 0033f0a15000 001e00000007 R_X86_64_JUMP_SLO 00000033f0807d10 _tr_align + 0 0033f0a15008 004800000007 R_X86_64_JUMP_SLO 00000033f0808db0 inflateReset + 0 0033f0a15010 000200000007 R_X86_64_JUMP_SLO 0000000000000000 memset + 0 0033f0a15018 000300000007 R_X86_64_JUMP_SLO 0000000000000000 ftell + 0 0033f0a15020 004f00000007 R_X86_64_JUMP_SLO 00000033f0807b70 _tr_stored_block + 0 0033f0a15028 005900000007 R_X86_64_JUMP_SLO 00000033f0808fd0 inflateEnd + 0 0033f0a15030 000400000007 R_X86_64_JUMP_SLO 0000000000000000 __fprintf_chk + 0 0033f0a15038 000700000007 R_X86_64_JUMP_SLO 0000000000000000 fseek + 0 0033f0a15040 002f00000007 R_X86_64_JUMP_SLO 00000033f0805b10 deflate + 0 0033f0a15048 006100000007 R_X86_64_JUMP_SLO 00000033f08032f0 gzrewind + 0 0033f0a15050 006900000007 R_X86_64_JUMP_SLO 00000033f0806c70 deflateInit_ + 0 0033f0a15058 000800000007 R_X86_64_JUMP_SLO 0000000000000000 malloc + 0 0033f0a15060 000900000007 R_X86_64_JUMP_SLO 0000000000000000 fopen + 0 0033f0a15068 006a00000007 R_X86_64_JUMP_SLO 00000033f0803b10 gzseek + 0 0033f0a15070 000a00000007 R_X86_64_JUMP_SLO 0000000000000000 __vsnprintf_chk + 0 0033f0a15078 002300000007 R_X86_64_JUMP_SLO 00000033f0808eb0 inflateInit2_ + 0 0033f0a15080 004600000007 R_X86_64_JUMP_SLO 00000033f08096f0 inflate + 0 0033f0a15088 000b00000007 R_X86_64_JUMP_SLO 0000000000000000 fputc + 0 0033f0a15090 000c00000007 R_X86_64_JUMP_SLO 0000000000000000 free + 0 0033f0a15098 004c00000007 R_X86_64_JUMP_SLO 00000033f0803180 gzwrite + 0 0033f0a150a0 000d00000007 R_X86_64_JUMP_SLO 0000000000000000 strlen + 0 0033f0a150a8 004700000007 R_X86_64_JUMP_SLO 00000033f0802680 compress2 + 0 0033f0a150b0 005300000007 R_X86_64_JUMP_SLO 00000033f0802780 crc32 + 0 0033f0a150b8 000e00000007 R_X86_64_JUMP_SLO 0000000000000000 ferror + 0 0033f0a150c0 005a00000007 R_X86_64_JUMP_SLO 00000033f08044f0 deflateEnd + 0 0033f0a150c8 000f00000007 R_X86_64_JUMP_SLO 0000000000000000 __cxa_finalize + 0 0033f0a150d0 006500000007 R_X86_64_JUMP_SLO 00000033f08067f0 deflateReset + 0 0033f0a150d8 001000000007 R_X86_64_JUMP_SLO 0000000000000000 fdopen + 0 0033f0a150e0 006e00000007 R_X86_64_JUMP_SLO 00000033f0806ca0 _tr_init + 0 0033f0a150e8 001100000007 R_X86_64_JUMP_SLO 0000000000000000 strerror + 0 0033f0a150f0 001200000007 R_X86_64_JUMP_SLO 0000000000000000 strcat + 0 0033f0a150f8 001300000007 R_X86_64_JUMP_SLO 0000000000000000 memcpy + 0 0033f0a15100 001400000007 R_X86_64_JUMP_SLO 0000000000000000 fread + 0 0033f0a15108 001500000007 R_X86_64_JUMP_SLO 0000000000000000 __errno_location + 0 0033f0a15110 001600000007 R_X86_64_JUMP_SLO 0000000000000000 __stack_chk_fail + 0 0033f0a15118 001700000007 R_X86_64_JUMP_SLO 0000000000000000 strcpy + 0 0033f0a15120 003600000007 R_X86_64_JUMP_SLO 00000033f0802660 compressBound + 0 0033f0a15128 005200000007 R_X86_64_JUMP_SLO 00000033f0808fc0 inflateInit_ + 0 0033f0a15130 003400000007 R_X86_64_JUMP_SLO 00000033f0806980 deflateInit2_ + 0 0033f0a15138 001800000007 R_X86_64_JUMP_SLO 0000000000000000 fclose + 0 0033f0a15140 002d00000007 R_X86_64_JUMP_SLO 00000033f08086c0 _tr_flush_block + 0 0033f0a15148 001900000007 R_X86_64_JUMP_SLO 0000000000000000 __sprintf_chk + 0 0033f0a15150 004500000007 R_X86_64_JUMP_SLO 00000033f08037f0 gzread + 0 0033f0a15158 001a00000007 R_X86_64_JUMP_SLO 0000000000000000 clearerr + 0 0033f0a15160 002c00000007 R_X86_64_JUMP_SLO 00000033f08021f0 adler32 + 0 0033f0a15168 001b00000007 R_X86_64_JUMP_SLO 0000000000000000 fwrite + 0 0033f0a15170 005700000007 R_X86_64_JUMP_SLO 00000033f080c870 inflate_table + 0 0033f0a15178 004900000007 R_X86_64_JUMP_SLO 00000033f08066a0 deflateParams + 0 0033f0a15180 003500000007 R_X86_64_JUMP_SLO 00000033f080cdd0 inflate_fast + 0 0033f0a15188 001c00000007 R_X86_64_JUMP_SLO 0000000000000000 fflush + 0 There are no unwind sections in this file. Symbol table '.dynsym' contains 112 entries: Num: Value Size Type Bind Vis Ndx Name 0: 0000000000000000 0 NOTYPE LOCAL DEFAULT UND 1: 00000033f0801dd0 0 SECTION LOCAL DEFAULT 10 2: 0000000000000000 0 FUNC GLOBAL DEFAULT UND memset@GLIBC_2.2.5 (8) 3: 0000000000000000 0 FUNC GLOBAL DEFAULT UND ftell@GLIBC_2.2.5 (8) 4: 0000000000000000 0 FUNC GLOBAL DEFAULT UND __fprintf_chk@GLIBC_2.3.4 (9) 5: 0000000000000000 0 NOTYPE WEAK DEFAULT UND __gmon_start__ 6: 0000000000000000 0 NOTYPE WEAK DEFAULT UND _Jv_RegisterClasses 7: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fseek@GLIBC_2.2.5 (8) 8: 0000000000000000 0 FUNC GLOBAL DEFAULT UND malloc@GLIBC_2.2.5 (8) 9: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fopen@GLIBC_2.2.5 (8) 10: 0000000000000000 0 FUNC GLOBAL DEFAULT UND __vsnprintf_chk@GLIBC_2.3.4 (9) 11: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fputc@GLIBC_2.2.5 (8) 12: 0000000000000000 0 FUNC GLOBAL DEFAULT UND free@GLIBC_2.2.5 (8) 13: 0000000000000000 0 FUNC GLOBAL DEFAULT UND strlen@GLIBC_2.2.5 (8) 14: 0000000000000000 0 FUNC GLOBAL DEFAULT UND ferror@GLIBC_2.2.5 (8) 15: 0000000000000000 0 FUNC WEAK DEFAULT UND __cxa_finalize@GLIBC_2.2.5 (8) 16: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fdopen@GLIBC_2.2.5 (8) 17: 0000000000000000 0 FUNC GLOBAL DEFAULT UND strerror@GLIBC_2.2.5 (8) 18: 0000000000000000 0 FUNC GLOBAL DEFAULT UND strcat@GLIBC_2.2.5 (8) 19: 0000000000000000 0 FUNC GLOBAL DEFAULT UND memcpy@GLIBC_2.2.5 (8) 20: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fread@GLIBC_2.2.5 (8) 21: 0000000000000000 0 FUNC GLOBAL DEFAULT UND __errno_location@GLIBC_2.2.5 (8) 22: 0000000000000000 0 FUNC GLOBAL DEFAULT UND __stack_chk_fail@GLIBC_2.4 (10) 23: 0000000000000000 0 FUNC GLOBAL DEFAULT UND strcpy@GLIBC_2.2.5 (8) 24: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fclose@GLIBC_2.2.5 (8) 25: 0000000000000000 0 FUNC GLOBAL DEFAULT UND __sprintf_chk@GLIBC_2.3.4 (9) 26: 0000000000000000 0 FUNC GLOBAL DEFAULT UND clearerr@GLIBC_2.2.5 (8) 27: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fwrite@GLIBC_2.2.5 (8) 28: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fflush@GLIBC_2.2.5 (8) 29: 00000033f0802570 240 FUNC GLOBAL DEFAULT 12 adler32_combine@@ZLIB_1.2.2 30: 00000033f0807d10 955 FUNC GLOBAL DEFAULT 12 _tr_align@@ZLIB_1.2.0 31: 00000033f08042c0 126 FUNC GLOBAL DEFAULT 12 gzdopen 32: 00000033f08092a0 42 FUNC GLOBAL DEFAULT 12 inflateSyncPoint 33: 00000033f08030b0 206 FUNC GLOBAL DEFAULT 12 gzclose 34: 00000033f080b510 52 FUNC GLOBAL DEFAULT 12 inflateBackEnd@@ZLIB_1.2.0 35: 00000033f0808eb0 268 FUNC GLOBAL DEFAULT 12 inflateInit2_ 36: 00000033f0802d10 42 FUNC GLOBAL DEFAULT 12 gzclearerr@@ZLIB_1.2.0.2 37: 00000033f08032c0 46 FUNC GLOBAL DEFAULT 12 gzputc 38: 00000033f08095e0 261 FUNC GLOBAL DEFAULT 12 inflateSetDictionary 39: 00000033f0802cf0 31 FUNC GLOBAL DEFAULT 12 gzdirect@@ZLIB_1.2.2.3 40: 00000033f0804350 235 FUNC GLOBAL DEFAULT 12 uncompress 41: 00000033f08033d0 284 FUNC GLOBAL DEFAULT 12 gzprintf 42: 00000033f0802a70 490 FUNC GLOBAL DEFAULT 12 crc32_combine@@ZLIB_1.2.2 43: 00000033f08080d0 165 FUNC GLOBAL DEFAULT 12 _tr_tally@@ZLIB_1.2.0 44: 00000033f08021f0 892 FUNC GLOBAL DEFAULT 12 adler32 45: 00000033f08086c0 1667 FUNC GLOBAL DEFAULT 12 _tr_flush_block@@ZLIB_1.2.0 46: 0000000000000000 0 OBJECT GLOBAL DEFAULT ABS ZLIB_1.2.0.2 47: 00000033f0805b10 2954 FUNC GLOBAL DEFAULT 12 deflate 48: 00000033f0804470 55 FUNC GLOBAL DEFAULT 12 deflatePrime@@ZLIB_1.2.0.8 49: 00000033f0804340 10 FUNC GLOBAL DEFAULT 12 gzopen 50: 00000033f080d3a8 0 FUNC GLOBAL DEFAULT 13 _fini@@ZLIB_1.2.0 51: 00000033f08067b0 62 FUNC GLOBAL DEFAULT 12 deflateBound@@ZLIB_1.2.0 52: 00000033f0806980 741 FUNC GLOBAL DEFAULT 12 deflateInit2_ 53: 00000033f080cdd0 1427 FUNC GLOBAL DEFAULT 12 inflate_fast@@ZLIB_1.2.0 54: 00000033f0802660 20 FUNC GLOBAL DEFAULT 12 compressBound@@ZLIB_1.2.0 55: 0000000000000000 0 OBJECT GLOBAL DEFAULT ABS ZLIB_1.2.0.8 56: 00000033f0811400 53 OBJECT GLOBAL DEFAULT 14 deflate_copyright@@ZLIB_1.2.0 57: 00000033f0809020 45 FUNC GLOBAL DEFAULT 12 inflateGetHeader@@ZLIB_1.2.2 58: 00000033f0813340 47 OBJECT GLOBAL DEFAULT 14 inflate_copyright@@ZLIB_1.2.0 59: 00000033f0801dd0 0 FUNC GLOBAL DEFAULT 10 _init@@ZLIB_1.2.0 60: 00000033f0808d60 6 FUNC GLOBAL DEFAULT 12 zlibCompileFlags@@ZLIB_1.2.0.2 61: 00000033f0803280 55 FUNC GLOBAL DEFAULT 12 gzputs 62: 00000033f0811440 512 OBJECT GLOBAL DEFAULT 14 _dist_code@@ZLIB_1.2.0 63: 00000033f0a14da0 80 OBJECT GLOBAL DEFAULT 20 z_errmsg@@ZLIB_1.2.0 64: 00000033f080b410 241 FUNC GLOBAL DEFAULT 12 inflateBackInit_@@ZLIB_1.2.0 65: 0000000000000000 0 OBJECT GLOBAL DEFAULT ABS ZLIB_1.2.0 66: 00000033f08092d0 398 FUNC GLOBAL DEFAULT 12 inflateCopy@@ZLIB_1.2.0 67: 0000000000000000 0 OBJECT GLOBAL DEFAULT ABS ZLIB_1.2.2 68: 00000033f08044b0 53 FUNC GLOBAL DEFAULT 12 deflateTune@@ZLIB_1.2.2.3 69: 00000033f08037f0 794 FUNC GLOBAL DEFAULT 12 gzread 70: 00000033f08096f0 7450 FUNC GLOBAL DEFAULT 12 inflate 71: 00000033f0802680 224 FUNC GLOBAL DEFAULT 12 compress2 72: 00000033f0808db0 161 FUNC GLOBAL DEFAULT 12 inflateReset 73: 00000033f08066a0 266 FUNC GLOBAL DEFAULT 12 deflateParams 74: 00000033f0802760 11 FUNC GLOBAL DEFAULT 12 compress 75: 00000033f0803e20 174 FUNC GLOBAL DEFAULT 12 gzsetparams 76: 00000033f0803180 249 FUNC GLOBAL DEFAULT 12 gzwrite 77: 00000033f0808da0 10 FUNC GLOBAL DEFAULT 12 zcalloc@@ZLIB_1.2.0 78: 00000033f0803390 63 FUNC GLOBAL DEFAULT 12 gzflush 79: 00000033f0807b70 407 FUNC GLOBAL DEFAULT 12 _tr_stored_block@@ZLIB_1.2.0 80: 00000033f0802c60 87 FUNC GLOBAL DEFAULT 12 gzungetc@@ZLIB_1.2.0.2 81: 00000033f0808d50 8 FUNC GLOBAL DEFAULT 12 zlibVersion 82: 00000033f0808fc0 15 FUNC GLOBAL DEFAULT 12 inflateInit_ 83: 00000033f0802780 744 FUNC GLOBAL DEFAULT 12 crc32 84: 00000033f0808d90 8 FUNC GLOBAL DEFAULT 12 zcfree@@ZLIB_1.2.0 85: 00000033f0809050 590 FUNC GLOBAL DEFAULT 12 inflateSync 86: 00000033f0804ea0 335 FUNC GLOBAL DEFAULT 12 deflateSetDictionary 87: 00000033f080c870 1368 FUNC GLOBAL DEFAULT 12 inflate_table@@ZLIB_1.2.0 88: 00000033f0802cc0 46 FUNC GLOBAL DEFAULT 12 gzeof 89: 00000033f0808fd0 78 FUNC GLOBAL DEFAULT 12 inflateEnd 90: 00000033f08044f0 263 FUNC GLOBAL DEFAULT 12 deflateEnd 91: 00000033f0803df0 41 FUNC GLOBAL DEFAULT 12 gzgetc 92: 00000033f0a15200 0 NOTYPE GLOBAL DEFAULT ABS _edata@@ZLIB_1.2.0 93: 00000033f0804440 38 FUNC GLOBAL DEFAULT 12 deflateSetHeader@@ZLIB_1.2.2 94: 00000033f0811640 256 OBJECT GLOBAL DEFAULT 14 _length_code@@ZLIB_1.2.0 95: 0000000000000000 0 OBJECT GLOBAL DEFAULT ABS ZLIB_1.2.2.3 96: 00000033f0803d40 12 FUNC GLOBAL DEFAULT 12 gztell 97: 00000033f08032f0 154 FUNC GLOBAL DEFAULT 12 gzrewind 98: 0000000000000000 0 OBJECT GLOBAL DEFAULT ABS ZLIB_1.2.2.4 99: 00000033f0808d70 21 FUNC GLOBAL DEFAULT 12 zError 100: 00000033f0a15210 0 NOTYPE GLOBAL DEFAULT ABS _end@@ZLIB_1.2.0 101: 00000033f08067f0 389 FUNC GLOBAL DEFAULT 12 deflateReset 102: 00000033f0804940 602 FUNC GLOBAL DEFAULT 12 deflateCopy 103: 00000033f080b550 4890 FUNC GLOBAL DEFAULT 12 inflateBack@@ZLIB_1.2.0 104: 00000033f0808e60 76 FUNC GLOBAL DEFAULT 12 inflatePrime@@ZLIB_1.2.2.4 105: 00000033f0806c70 41 FUNC GLOBAL DEFAULT 12 deflateInit_ 106: 00000033f0803b10 560 FUNC GLOBAL DEFAULT 12 gzseek 107: 00000033f0802d40 307 FUNC GLOBAL DEFAULT 12 gzerror 108: 00000033f0a15200 0 NOTYPE GLOBAL DEFAULT ABS __bss_start@@ZLIB_1.2.0 109: 00000033f0802770 8 FUNC GLOBAL DEFAULT 12 get_crc_table 110: 00000033f0806ca0 248 FUNC GLOBAL DEFAULT 12 _tr_init@@ZLIB_1.2.0 111: 00000033f0803d50 151 FUNC GLOBAL DEFAULT 12 gzgets Histogram for `.gnu.hash' bucket list length (total of 67 buckets): Length Number % of total Coverage 0 17 ( 25.4%) 1 23 ( 34.3%) 27.7% 2 23 ( 34.3%) 83.1% 3 3 ( 4.5%) 94.0% 4 0 ( 0.0%) 94.0% 5 1 ( 1.5%) 100.0% Version symbols section '.gnu.version' contains 112 entries: Addr: 00000033f08013de Offset: 0x0013de Link: 3 (.dynsym) 000: 0 (*local*) 0 (*local*) 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) 004: 9 (GLIBC_2.3.4) 0 (*local*) 0 (*local*) 8 (GLIBC_2.2.5) 008: 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) 9 (GLIBC_2.3.4) 8 (GLIBC_2.2.5) 00c: 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) 010: 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) 014: 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) a (GLIBC_2.4) 8 (GLIBC_2.2.5) 018: 8 (GLIBC_2.2.5) 9 (GLIBC_2.3.4) 8 (GLIBC_2.2.5) 8 (GLIBC_2.2.5) 01c: 8 (GLIBC_2.2.5) 5 (ZLIB_1.2.2) 2 (ZLIB_1.2.0) 1 (*global*) 020: 1 (*global*) 1 (*global*) 2 (ZLIB_1.2.0) 1 (*global*) 024: 3 (ZLIB_1.2.0.2) 1 (*global*) 1 (*global*) 6 (ZLIB_1.2.2.3) 028: 1 (*global*) 1 (*global*) 5 (ZLIB_1.2.2) 2 (ZLIB_1.2.0) 02c: 1 (*global*) 2 (ZLIB_1.2.0) 3 (ZLIB_1.2.0.2) 1 (*global*) 030: 4 (ZLIB_1.2.0.8) 1 (*global*) 2 (ZLIB_1.2.0) 2 (ZLIB_1.2.0) 034: 1 (*global*) 2 (ZLIB_1.2.0) 2 (ZLIB_1.2.0) 4 (ZLIB_1.2.0.8) 038: 2 (ZLIB_1.2.0) 5 (ZLIB_1.2.2) 2 (ZLIB_1.2.0) 2 (ZLIB_1.2.0) 03c: 3 (ZLIB_1.2.0.2) 1 (*global*) 2 (ZLIB_1.2.0) 2 (ZLIB_1.2.0) 040: 2 (ZLIB_1.2.0) 2 (ZLIB_1.2.0) 2 (ZLIB_1.2.0) 5 (ZLIB_1.2.2) 044: 6 (ZLIB_1.2.2.3) 1 (*global*) 1 (*global*) 1 (*global*) 048: 1 (*global*) 1 (*global*) 1 (*global*) 1 (*global*) 04c: 1 (*global*) 2 (ZLIB_1.2.0) 1 (*global*) 2 (ZLIB_1.2.0) 050: 3 (ZLIB_1.2.0.2) 1 (*global*) 1 (*global*) 1 (*global*) 054: 2 (ZLIB_1.2.0) 1 (*global*) 1 (*global*) 2 (ZLIB_1.2.0) 058: 1 (*global*) 1 (*global*) 1 (*global*) 1 (*global*) 05c: 2 (ZLIB_1.2.0) 5 (ZLIB_1.2.2) 2 (ZLIB_1.2.0) 6 (ZLIB_1.2.2.3) 060: 1 (*global*) 1 (*global*) 7 (ZLIB_1.2.2.4) 1 (*global*) 064: 2 (ZLIB_1.2.0) 1 (*global*) 1 (*global*) 2 (ZLIB_1.2.0) 068: 7 (ZLIB_1.2.2.4) 1 (*global*) 1 (*global*) 1 (*global*) 06c: 2 (ZLIB_1.2.0) 1 (*global*) 2 (ZLIB_1.2.0) 1 (*global*) Version definition section '.gnu.version_d' contains 7 entries: Addr: 0x00000033f08014c0 Offset: 0x0014c0 Link: 4 (.dynstr) 000000: Rev: 1 Flags: BASE Index: 1 Cnt: 1 Name: libz.so.1 0x001c: Rev: 1 Flags: none Index: 2 Cnt: 1 Name: ZLIB_1.2.0 0x0038: Rev: 1 Flags: none Index: 3 Cnt: 2 Name: ZLIB_1.2.0.2 0x0054: Parent 1: ZLIB_1.2.0 0x005c: Rev: 1 Flags: none Index: 4 Cnt: 2 Name: ZLIB_1.2.0.8 0x0078: Parent 1: ZLIB_1.2.0.2 0x0080: Rev: 1 Flags: none Index: 5 Cnt: 2 Name: ZLIB_1.2.2 0x009c: Parent 1: ZLIB_1.2.0.8 0x00a4: Rev: 1 Flags: none Index: 6 Cnt: 2 Name: ZLIB_1.2.2.3 0x00c0: Parent 1: ZLIB_1.2.2 0x00c8: Rev: 1 Flags: none Index: 7 Cnt: 2 Name: ZLIB_1.2.2.4 0x00e4: Parent 1: ZLIB_1.2.2.3 Version needs section '.gnu.version_r' contains 1 entries: Addr: 0x00000033f08015b0 Offset: 0x0015b0 Link: 4 (.dynstr) 000000: Version: 1 File: libc.so.6 Cnt: 3 0x0010: Name: GLIBC_2.4 Flags: none Version: 10 0x0020: Name: GLIBC_2.3.4 Flags: none Version: 9 0x0030: Name: GLIBC_2.2.5 Flags: none Version: 8 Notes at offset 0x000001c8 with length 0x00000024: Owner Data size Description GNU 0x00000014 NT_GNU_BUILD_ID (unique build ID bitstring) Library list section '.gnu.liblist' contains 2 entries: Library Time Stamp Checksum Version Flags 0: libc.so.6 2016-02-23T09:02:06 0xe2c58dbe 0 0 1: /lib64/ld-linux-x86- 2016-02-23T09:02:06 0xcb4dfea2 0 0 Here is what’s missing next to the blue text : 66: 00000000000101c0 13 FUNC GLOBAL DEFAULT 12 gzopen64@@ZLIB_1.2.3.3 What do you guys think about this???? Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 I Bur. : 1-514-343-6111 poste 16568 -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: May-26-16 3:32 AM To: Fernandez Edgar <edgar.fernandez@umontreal.ca>; Nate Coraor <nate@bx.psu.edu> Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] not sure what I can do about this... Sorry Edgar, It looks like something else is causing this error (and my guess about different versions of Linux on Galaxy and the cluster was wrong): ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64 It may be important how the pysam wheel was compiled, perhaps Nate may be able to comment (CC'd). Peter On Wed, May 25, 2016 at 12:40 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca<mailto:edgar.fernandez@umontreal.ca>> wrote:
Hello Peter,
For now, my new installation of galaxy v16.01 is on one test desktop running Oracle Linux 6.
Before changing my production installation, I'm doing my due diligent.
Let me know what you think...
Edgar Fernandez
Hey guys, I successfully fixed my problem. Here's the solution if you would like to know: 1. download zlib-1.2.8.tar.gz 2. ./configure --prefix=/usr/local/zlib-1.2.8 3. make 4. make install 5. add the following in the file config/local_env.sh export LD_LIBRARY_PATH=/usr/local/zlib-1.2.8${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}} Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 I Bur. : 1-514-343-6111 poste 16568 -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: May-26-16 3:32 AM To: Fernandez Edgar <edgar.fernandez@umontreal.ca>; Nate Coraor <nate@bx.psu.edu> Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] not sure what I can do about this... Sorry Edgar, It looks like something else is causing this error (and my guess about different versions of Linux on Galaxy and the cluster was wrong): ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: gzopen64 It may be important how the pysam wheel was compiled, perhaps Nate may be able to comment (CC'd). Peter On Wed, May 25, 2016 at 12:40 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:
Hello Peter,
For now, my new installation of galaxy v16.01 is on one test desktop running Oracle Linux 6. Before changing my production installation, I'm doing my due diligent.
Let me know what you think...
Edgar Fernandez
participants (7)
-
Björn Grüning -
Eric Rasche -
Fernandez Edgar -
Marius van den Beek -
Nicola Soranzo -
Peter Cock -
Philip Mabon