Hi there,
Hope this mail will find you in sound. I was trying to install dlcpar in my linux workstation. I failed everytime. I was trying in many ways but still no luck. Here are the error messages:
But,
When I tried to run orthofinder, it works fine, finding all the dependencies but not dlcpar.
Any suggestion for me?
Best Regards
Zillur
Hope this mail will find you in sound. I was trying to install dlcpar in my linux workstation. I failed everytime. I was trying in many ways but still no luck. Here are the error messages:
Code:
[zillur@genomics dlcpar-master]$ python setup.py install --home=~ running install running build running build_py running build_scripts running install_lib creating /home/zillur/lib creating /home/zillur/lib/python creating /home/zillur/lib/python/dlcpar copying build/lib/dlcpar/__init__.py -> /home/zillur/lib/python/dlcpar copying build/lib/dlcpar/common.py -> /home/zillur/lib/python/dlcpar copying build/lib/dlcpar/countvector.py -> /home/zillur/lib/python/dlcpar copying build/lib/dlcpar/recon.py -> /home/zillur/lib/python/dlcpar copying build/lib/dlcpar/reconlib.py -> /home/zillur/lib/python/dlcpar copying build/lib/dlcpar/reconscape.py -> /home/zillur/lib/python/dlcpar copying build/lib/dlcpar/simplerecon.py -> /home/zillur/lib/python/dlcpar creating /home/zillur/lib/python/dlcpar/deps creating /home/zillur/lib/python/dlcpar/deps/rasmus copying build/lib/dlcpar/deps/rasmus/__init__.py -> /home/zillur/lib/python/dlcpar/deps/rasmus copying build/lib/dlcpar/deps/rasmus/linked_list.py -> /home/zillur/lib/python/dlcpar/deps/rasmus copying build/lib/dlcpar/deps/rasmus/plotting.py -> /home/zillur/lib/python/dlcpar/deps/rasmus copying build/lib/dlcpar/deps/rasmus/stats.py -> /home/zillur/lib/python/dlcpar/deps/rasmus copying build/lib/dlcpar/deps/rasmus/tablelib.py -> /home/zillur/lib/python/dlcpar/deps/rasmus copying build/lib/dlcpar/deps/rasmus/textdraw.py -> /home/zillur/lib/python/dlcpar/deps/rasmus copying build/lib/dlcpar/deps/rasmus/timer.py -> /home/zillur/lib/python/dlcpar/deps/rasmus copying build/lib/dlcpar/deps/rasmus/treelib.py -> /home/zillur/lib/python/dlcpar/deps/rasmus copying build/lib/dlcpar/deps/rasmus/util.py -> /home/zillur/lib/python/dlcpar/deps/rasmus creating /home/zillur/lib/python/dlcpar/deps/compbio copying build/lib/dlcpar/deps/compbio/__init__.py -> /home/zillur/lib/python/dlcpar/deps/compbio copying build/lib/dlcpar/deps/compbio/birthdeath.py -> /home/zillur/lib/python/dlcpar/deps/compbio copying build/lib/dlcpar/deps/compbio/coal.py -> /home/zillur/lib/python/dlcpar/deps/compbio copying build/lib/dlcpar/deps/compbio/fasta.py -> /home/zillur/lib/python/dlcpar/deps/compbio copying build/lib/dlcpar/deps/compbio/phylo.py -> /home/zillur/lib/python/dlcpar/deps/compbio copying build/lib/dlcpar/deps/compbio/phyloDLC.py -> /home/zillur/lib/python/dlcpar/deps/compbio copying build/lib/dlcpar/deps/compbio/seqlib.py -> /home/zillur/lib/python/dlcpar/deps/compbio byte-compiling /home/zillur/lib/python/dlcpar/__init__.py to __init__.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/common.py to common.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/countvector.py to countvector.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/recon.py to recon.cpython-35.pyc File "/home/zillur/lib/python/dlcpar/recon.py", line 213 subtrees_snode.sort(key=lambda (root, rootchild, leaves): ids[root.name]) ^ SyntaxError: invalid syntax byte-compiling /home/zillur/lib/python/dlcpar/reconlib.py to reconlib.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/reconscape.py to reconscape.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/simplerecon.py to simplerecon.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/__init__.py to __init__.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/linked_list.py to linked_list.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/plotting.py to plotting.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/stats.py to stats.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/tablelib.py to tablelib.cpython-35.pyc File "/home/zillur/lib/python/dlcpar/deps/rasmus/tablelib.py", line 353 except Exception, e: ^ SyntaxError: invalid syntax byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/textdraw.py to textdraw.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/timer.py to timer.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/treelib.py to treelib.cpython-35.pyc File "/home/zillur/lib/python/dlcpar/deps/rasmus/treelib.py", line 1088 print i, parentid ^ SyntaxError: Missing parentheses in call to 'print' byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/util.py to util.cpython-35.pyc File "/home/zillur/lib/python/dlcpar/deps/rasmus/util.py", line 114 print str(j) + ", ", ^ SyntaxError: invalid syntax byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/__init__.py to __init__.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/birthdeath.py to birthdeath.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/coal.py to coal.cpython-35.pyc File "/home/zillur/lib/python/dlcpar/deps/compbio/coal.py", line 1608 print p, N, t ^ SyntaxError: Missing parentheses in call to 'print' byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/fasta.py to fasta.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/phylo.py to phylo.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/phyloDLC.py to phyloDLC.cpython-35.pyc byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/seqlib.py to seqlib.cpython-35.pyc running install_scripts creating /home/zillur/bin copying build/scripts-3.5/dlcpar -> /home/zillur/bin copying build/scripts-3.5/dlcpar_search -> /home/zillur/bin copying build/scripts-3.5/dlcoal_to_dlcpar -> /home/zillur/bin copying build/scripts-3.5/dlcpar_to_dlcoal -> /home/zillur/bin copying build/scripts-3.5/tree-events-dlc -> /home/zillur/bin copying build/scripts-3.5/tree-events-dlcpar -> /home/zillur/bin changing mode of /home/zillur/bin/dlcpar to 775 changing mode of /home/zillur/bin/dlcpar_search to 775 changing mode of /home/zillur/bin/dlcoal_to_dlcpar to 775 changing mode of /home/zillur/bin/dlcpar_to_dlcoal to 775 changing mode of /home/zillur/bin/tree-events-dlc to 775 changing mode of /home/zillur/bin/tree-events-dlcpar to 775 running install_egg_info Writing /home/zillur/lib/python/dlcpar-1.0.1-py3.5.egg-info
Code:
[zillur@genomics dlcpar-master]$ cd /home/zillur/bin/ [zillur@genomics bin]$ ls dlcoal_to_dlcpar dlcpar dlcpar_search dlcpar_to_dlcoal tree-events-dlc tree-events-dlcpar [zillur@genomics bin]$ ./dlcpar Traceback (most recent call last): File "./dlcpar", line 10, in <module> import dlcpar ImportError: No module named 'dlcpar'"
Code:
Test can run "fastme -i /home/zillur/Desktop/zillur/phd/orthofinder/fasta/test/Results_Nov23/WorkingDirectory/SimpleTest.phy -o /home/zillur/Desktop/zillur/phd/orthofinder/fasta/test/Results_Nov23/WorkingDirectory/SimpleTest.tre" - ok Test can run "dlcpar_search --version" - failed ERROR: Cannot run dlcpar_search Please check DLCpar is installed and that the executables are in the system path. Orthogroups have been inferred but the dependencies for inferring gene trees and orthologues have not been met. Please review previous messages for more information
Best Regards
Zillur