Hi - I&#39;ve just finished installing a ROCKS 5.4.3 cluster and am now adding Galaxy to it.  We are using torque instead of SGE.  I see the Wiki docs at <a href="http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster">http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster</a> state I need to scramble pbs_python by doing:<div>
<br></div><div>LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python</div><div><br></div><div>I have libtorque installed in /usr/lib64:</div><div><br></div><div><div>[galaxy@bic x86_64]$ ll /usr/lib64/libtorque.*</div>
<div>-rw-r--r-- 1 root root 536862 Dec 28 12:32 /usr/lib64/libtorque.a</div><div>-rwxr-xr-x 1 root root    810 Dec 28 12:32 /usr/lib64/<a href="http://libtorque.la">libtorque.la</a></div><div>lrwxrwxrwx 1 root root     18 Dec 28 13:50 /usr/lib64/libtorque.so -&gt; libtorque.so.2.0.0</div>
<div>lrwxrwxrwx 1 root root     14 Dec 28 13:50 /usr/lib64/libtorque.so.0 -&gt; libtorque.so.2</div><div>lrwxrwxrwx 1 root root     18 Dec 28 13:50 /usr/lib64/libtorque.so.2 -&gt; libtorque.so.2.0.0</div><div>-rwxr-xr-x 1 root root 766431 Dec 28 12:32 /usr/lib64/libtorque.so.2.0.0</div>
</div><div><br></div><div>So I then run (and get the error shown at the bottom):</div><div><div>[galaxy@bic x86_64]$ cd</div><div>[galaxy@bic ~]$ cd galaxy-dist/</div><div>[galaxy@bic galaxy-dist]$ LIBTORQUE_DIR=/usr/lib64/libtorque.so.2.0.0 python scripts/scramble.py -e pbs_python</div>
<div>fetch_one(): Trying to fetch:</div><div>  <a href="http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz">http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz</a></div><div>fetch_one(): Fetched to:</div>
<div>  /home/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.1.0.tar.gz</div><div>unpack_source(): Unpacked to:</div><div>  /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python</div>
<div>copy_build_script(): Using build script /home/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py</div><div>run_scramble_script(): Beginning build</div><div>run_scramble_script(): Executing in /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python:</div>
<div>  /share/apps/Python-2.6.7/bin/python scramble.py</div><div><br></div><div>---------------------------------------------------------------------------</div><div>This script requires setuptools version 0.6c11 to run (even to display</div>
<div>help).  I will attempt to download it for you (from</div><div><a href="http://pypi.python.org/packages/2.6/s/setuptools/">http://pypi.python.org/packages/2.6/s/setuptools/</a>), but</div><div>you may need to enable firewall access for this script first.</div>
<div>I will start the download in 8 seconds.</div><div><br></div><div>(Note: if this machine does not have network access, please obtain the file</div><div><br></div><div>   <a href="http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg">http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg</a></div>
<div><br></div><div>and place it in this directory before rerunning this script.)</div><div>---------------------------------------------------------------------------</div><div>Downloading <a href="http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg">http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg</a></div>
<div>checking for pbs-config... /usr/bin/pbs-config</div><div>Found torque version: 2.5.9</div><div>checking for python... /share/apps/Python-2.6.7/bin/python</div><div>checking for python version... 2.6</div><div>checking for python platform... linux2</div>
<div>checking for python script directory... ${prefix}/lib/python2.6/site-packages</div><div>checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages</div><div>configure: creating ./config.status</div>
<div>config.status: creating Makefile</div><div>config.status: creating setup.py</div><div>scramble(): Patching setup.py</div><div>running egg_info</div><div>creating src/pbs_python.egg-info</div><div>writing src/pbs_python.egg-info/PKG-INFO</div>
<div>writing top-level names to src/pbs_python.egg-info/top_level.txt</div><div>writing dependency_links to src/pbs_python.egg-info/dependency_links.txt</div><div>writing manifest file &#39;src/pbs_python.egg-info/SOURCES.txt&#39;</div>
<div>reading manifest file &#39;src/pbs_python.egg-info/SOURCES.txt&#39;</div><div>writing manifest file &#39;src/pbs_python.egg-info/SOURCES.txt&#39;</div><div>running bdist_egg</div><div>installing library code to build/bdist.linux-x86_64/egg</div>
<div>running install_lib</div><div>running build_py</div><div>creating build</div><div>creating build/lib.linux-x86_64-2.6</div><div>copying src/pbs.py -&gt; build/lib.linux-x86_64-2.6</div><div>copying src/PBSQuery.py -&gt; build/lib.linux-x86_64-2.6</div>
<div>running build_ext</div><div>building &#39;_pbs&#39; extension</div><div>creating build/temp.linux-x86_64-2.6</div><div>creating build/temp.linux-x86_64-2.6/src</div><div>gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DTORQUE_2_4 -I/share/apps/Python-2.6.7/include/python2.6 -c src/pbs_wrap.c -o build/temp.linux-x86_64-2.6/src/pbs_wrap.o</div>
<div>src/pbs_wrap.c:2622: warning: function declaration isn&#39;t a prototype</div><div>src/pbs_wrap.c:2630: warning: function declaration isn&#39;t a prototype</div><div>gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o -L/usr/lib64 -ltorque -o build/lib.linux-x86_64-2.6/_pbs.so</div>
<div>creating build/bdist.linux-x86_64</div><div>creating build/bdist.linux-x86_64/egg</div><div>copying build/lib.linux-x86_64-2.6/pbs.py -&gt; build/bdist.linux-x86_64/egg</div><div>copying build/lib.linux-x86_64-2.6/PBSQuery.py -&gt; build/bdist.linux-x86_64/egg</div>
<div>copying build/lib.linux-x86_64-2.6/_pbs.so -&gt; build/bdist.linux-x86_64/egg</div><div>byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc</div><div>byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc</div>
<div>creating stub loader for _pbs.so</div><div>byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc</div><div>creating build/bdist.linux-x86_64/egg/EGG-INFO</div><div>copying src/pbs_python.egg-info/PKG-INFO -&gt; build/bdist.linux-x86_64/egg/EGG-INFO</div>
<div>copying src/pbs_python.egg-info/SOURCES.txt -&gt; build/bdist.linux-x86_64/egg/EGG-INFO</div><div>copying src/pbs_python.egg-info/dependency_links.txt -&gt; build/bdist.linux-x86_64/egg/EGG-INFO</div><div>copying src/pbs_python.egg-info/top_level.txt -&gt; build/bdist.linux-x86_64/egg/EGG-INFO</div>
<div>writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt</div><div>zip_safe flag not set; analyzing archive contents...</div><div>creating dist</div><div>creating &#39;dist/pbs_python-4.1.0-py2.6-linux-x86_64.egg&#39; and adding &#39;build/bdist.linux-x86_64/egg&#39; to it</div>
<div>removing &#39;build/bdist.linux-x86_64/egg&#39; (and everything under it)</div><div>Traceback (most recent call last):</div><div>  File &quot;scripts/scramble.py&quot;, line 50, in &lt;module&gt;</div><div>    egg.scramble()</div>
<div>  File &quot;/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py&quot;, line 60, in scramble</div><div>    raise ScrambleFailure( self, &quot;%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n  %s&quot; % ( sys._getframe().f_code.co_name, <a href="http://self.name">self.name</a>, new_egg ) )</div>
<div>galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pbs_python did not appear to fail, but no egg found to copy from expected path:</div><div>  /home/galaxy/galaxy-dist/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python/dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs2.egg</div>
<div>[galaxy@bic galaxy-dist]$ cd scripts/scramble</div><div>[galaxy@bic scramble]$ ll</div><div>total 20</div><div>drwxrwxr-x 2 galaxy galaxy 4096 Dec 29 16:21 archives</div><div>drwxrwxr-x 3 galaxy galaxy 4096 Dec 29 16:21 build</div>
<div>drwxrwxr-x 2 galaxy galaxy 4096 Dec 29 16:22 lib</div><div>drwxrwxr-x 7 galaxy galaxy 4096 Dec 29 13:25 patches</div><div>drwxrwxr-x 2 galaxy galaxy 4096 Dec 29 13:25 scripts</div><div>[galaxy@bic scramble]$ cd build/</div>
<div>[galaxy@bic build]$ ll</div><div>total 4</div><div>drwxrwxr-x 3 galaxy galaxy 4096 Dec 29 16:21 py2.6-linux-x86_64-ucs2</div><div>[galaxy@bic build]$ cd py2.6-linux-x86_64-ucs2/</div><div>[galaxy@bic py2.6-linux-x86_64-ucs2]$ ll</div>
<div>total 4</div><div>drwx------ 7 galaxy galaxy 4096 Dec 29 16:22 pbs_python</div><div>[galaxy@bic py2.6-linux-x86_64-ucs2]$ cd pbs_python/dist/</div><div>[galaxy@bic dist]$ ll</div><div>total 180</div><div>-rw-rw-r-- 1 galaxy galaxy 178869 Dec 29 16:22 pbs_python-4.1.0-py2.6-linux-x86_64.egg</div>
</div><div><br></div><div><br></div><div>I see the egg is created, but not with the name expected by galaxy.  How do I fix this?</div><div><br></div><div><br></div>