Installation fails due to python's "SyntaxError: invalid syntax"

[mmokrejs]

Which python versions are supported please?

byte-compiling /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/_python3.5/usr/lib64/python3.5/site-packages/oncotator/get_footprints.py to get_footprints.cpython-35.pyc
byte-compiling /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/_python3.5/usr/lib64/python3.5/site-packages/oncotator/downloadENSEMBL.py to downloadENSEMBL.cpython-35.pyc
writing byte-compilation script '/scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/temp/tmp_xk5nfoc.py'
/usr/bin/python3.5 -O /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/temp/tmp_xk5nfoc.py
  File "/usr/lib64/python3.5/site-packages/oncotator/datasources/ReferenceDatasource.py", line 155
    if f.find(tmp)<> -1:
                   ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/index/gaf.py", line 90
    print j
          ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/index/create_cosmic_ds_file.py", line 75
    print "Loading cosmic data..."
                                 ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/index/create_tcga_ds_file.py", line 65
    print "Loading tcga data..."
                               ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/ConfigUtils.py", line 183
    if configLocalSourceFP <> None:
                            ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/db.py", line 132
    if len(set(colnames).intersection(set(indexColumnList))) <> len(set(indexColumnList)):
                                                              ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/install/GenomeBuildInstallUtils.py", line 151
    print "Now Downloading {0}...".format(gtf_file)
                                 ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/MutUtils.py", line 282
    print mutation[annotation]
                 ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/Gaf.py", line 138
    print line
             ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/MutationData.py", line 177
    print "Datasource -- Annotation -- Annotation Value"
                                                       ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/oncotator-index.py", line 60
    print "Usage: oncotator-index <gaf|gaf-seqs|cosmic> <input_file> <version>"
                                                                              ^
SyntaxError: Missing parentheses in call to 'print'

removing /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/temp/tmp_xk5nfoc.py
writing byte-compilation script '/scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/temp/tmpoi1pbplc.py'
/usr/bin/python3.5 -OO /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/temp/tmpoi1pbplc.py
  File "/usr/lib64/python3.5/site-packages/oncotator/datasources/ReferenceDatasource.py", line 155
    if f.find(tmp)<> -1:
                   ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/index/gaf.py", line 90
    print j
          ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/index/create_cosmic_ds_file.py", line 75
    print "Loading cosmic data..."
                                 ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/index/create_tcga_ds_file.py", line 65
    print "Loading tcga data..."
                               ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/ConfigUtils.py", line 183
    if configLocalSourceFP <> None:
                            ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/db.py", line 132
    if len(set(colnames).intersection(set(indexColumnList))) <> len(set(indexColumnList)):
                                                              ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/install/GenomeBuildInstallUtils.py", line 151
    print "Now Downloading {0}...".format(gtf_file)
                                 ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/MutUtils.py", line 282
    print mutation[annotation]
                 ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/Gaf.py", line 138
    print line
             ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/MutationData.py", line 177
    print "Datasource -- Annotation -- Annotation Value"
                                                       ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/oncotator-index.py", line 60
    print "Usage: oncotator-index <gaf|gaf-seqs|cosmic> <input_file> <version>"
                                                                              ^
SyntaxError: Missing parentheses in call to 'print'

removing /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/temp/tmpoi1pbplc.py
running install_egg_info
Copying Oncotator.egg-info to /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/_python3.5/usr/lib64/python3.5/site-packages/Oncotator-1.9.1.0-py3.5.egg-info
running install_scripts
Installing Oncotator script to /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/_python3.5/usr/lib/python-exec/python3.5
Installing initializeTranscriptDatasource script to /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/_python3.5/usr/lib/python-exec/python3.5
Installing initializeDatasource script to /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/_python3.5/usr/lib/python-exec/python3.5
Installing addDatasourceMd5 script to /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/_python3.5/usr/lib/python-exec/python3.5
Installing get_exons script to /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/_python3.5/usr/lib/python-exec/python3.5
Installing oncotator script to /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/_python3.5/usr/lib/python-exec/python3.5
/usr/lib64/python3.5/site-packages/setuptools/dist.py:334: UserWarning: Normalizing 'v1.9.1.0' to '1.9.1.0'
  normalized_version,
  File "/usr/lib64/python3.5/site-packages/oncotator/datasources/ReferenceDatasource.py", line 155
    if f.find(tmp)<> -1:
                   ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/index/gaf.py", line 90
    print j
          ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/index/create_cosmic_ds_file.py", line 75
    print "Loading cosmic data..."
                                 ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/index/create_tcga_ds_file.py", line 65
    print "Loading tcga data..."
                               ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/ConfigUtils.py", line 183
    if configLocalSourceFP <> None:
                            ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/db.py", line 132
    if len(set(colnames).intersection(set(indexColumnList))) <> len(set(indexColumnList)):
                                                              ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/install/GenomeBuildInstallUtils.py", line 151
    print "Now Downloading {0}...".format(gtf_file)
                                 ^
SyntaxError: invalid syntax

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/MutUtils.py", line 282
    print mutation[annotation]
                 ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/utils/Gaf.py", line 138
    print line
             ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/MutationData.py", line 177
    print "Datasource -- Annotation -- Annotation Value"
                                                       ^
SyntaxError: Missing parentheses in call to 'print'

  File "/usr/lib64/python3.5/site-packages/oncotator/oncotator-index.py", line 60
    print "Usage: oncotator-index <gaf|gaf-seqs|cosmic> <input_file> <version>"
                                                                              ^
SyntaxError: Missing parentheses in call to 'print'

ngslib must be installed manually on non-mac: pip install --no-binary :all: ngslib==1.1.18
 * python3_5: running distutils-r1_run_phase distutils-r1_python_install_all
>>> Completed installing oncotator-1.9.2.0 into /scratch/var/tmp/portage/sci-biology/oncotator-1.9.2.0/image/

[lbergelson]

@mmokrejs python 2.7 is supported. Unfortunately we don't support 3+.