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Issues in setup.py #30

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niemasd opened this issue Apr 15, 2018 · 10 comments
Open

Issues in setup.py #30

niemasd opened this issue Apr 15, 2018 · 10 comments

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@niemasd
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niemasd commented Apr 15, 2018

In the README, in step 5 (run sudo python setup.py develop), I think the setup.py script is expecting Python 3, because I get the following error message:

Traceback (most recent call last):
  File "setup.py", line 14, in <module>
    ez_setup.use_setuptools()
  File "/root/pasta/ez_setup.py", line 98, in use_setuptools
    return do_download()       
  File "/root/pasta/ez_setup.py", line 92, in do_download
    egg = download_setuptools(version, download_base, to_dir, download_delay)
  File "/root/pasta/ez_setup.py", line 127, in download_setuptools
    import urllib.request, urllib.error, urllib.parse, shutil
ImportError: No module named request

In Python 2, it's urllib2.request, not urllib.request, which is why I think it's expecting Python 3. I think this holds true for the other urllib things being imported too (https://docs.python.org/2/library/urllib.html). It might be good to add a version check or perhaps a try-except block, e.g.:

try: # Python 3
    import urllib.request, urllib.error, urllib.parse, shutil
except: # Python 2
    # do whatever the correct thing is in Python 2
@niemasd niemasd changed the title setup.py expects Python 3? Issues in setup.py Apr 15, 2018
@niemasd
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niemasd commented Apr 15, 2018

Now, trying Python 3 (i.e., sudo python3 setup.py develop), I get the following error:

  File "setup.py", line 200
    fullPath = os.path.join(searchDir, files)
                                            ^
TabError: inconsistent use of tabs and spaces in indentation

It seems like it might be a good idea to overall check the setup.py script

@niemasd
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niemasd commented Apr 15, 2018

Fixed tab/space issue: 22e855f

Haven't attempted to fix the urllib import error

@niemasd
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niemasd commented Apr 15, 2018

Now (in Python 3) the setup.py script starts at makes progress, but it errors out like this:

Creating link: '/usr/local/bin/pasta/resources/scripts/hmmeralign' => '/usr/local/bin/pasta/bin/hmmeralign'
Creating link: '/usr/local/bin/sate-tools-linux/randtree' => '/usr/local/bin/pasta/bin/randtree'
Creating link: '/usr/local/bin/sate-tools-linux/opal.jar' => '/usr/local/bin/pasta/bin/opal.jar'
Creating link: '/usr/local/bin/sate-tools-linux/fasttreeMP' => '/usr/local/bin/pasta/bin/fasttreeMP'
Creating link: '/usr/local/bin/sate-tools-linux/muscle' => '/usr/local/bin/pasta/bin/muscle'
Creating link: '/usr/local/bin/sate-tools-linux/fakealigner' => '/usr/local/bin/pasta/bin/fakealigner'
Creating link: '/usr/local/bin/sate-tools-linux/clustalw2' => '/usr/local/bin/pasta/bin/clustalw2'
Creating link: '/usr/local/bin/sate-tools-linux/.gitignore' => '/usr/local/bin/pasta/bin/.gitignore'
Creating link: '/usr/local/bin/sate-tools-linux/fasttree' => '/usr/local/bin/pasta/bin/fasttree'
Creating link: '/usr/local/bin/sate-tools-linux/raxml' => '/usr/local/bin/pasta/bin/raxml'
Creating link: '/usr/local/bin/sate-tools-linux/contralign' => '/usr/local/bin/pasta/bin/contralign'
Creating link: '/usr/local/bin/sate-tools-linux/mafft' => '/usr/local/bin/pasta/bin/mafft'
Creating link: '/usr/local/bin/sate-tools-linux/contralign.topology' => '/usr/local/bin/pasta/bin/contralign.topology'
Creating link: '/usr/local/bin/sate-tools-linux/raxmlp' => '/usr/local/bin/pasta/bin/raxmlp'
Creating link: '/usr/local/bin/sate-tools-linux/faketree' => '/usr/local/bin/pasta/bin/faketree'
Creating link: '/usr/local/bin/sate-tools-linux/padaligner' => '/usr/local/bin/pasta/bin/padaligner'
Creating link: '/usr/local/bin/sate-tools-linux/homologs' => '/usr/local/bin/pasta/bin/homologs'
Creating link: '/usr/local/bin/sate-tools-linux/prank' => '/usr/local/bin/pasta/bin/prank'
Creating link: '/usr/local/bin/sate-tools-linux/hmmalign' => '/usr/local/bin/pasta/bin/hmmalign'
Creating link: '/usr/local/bin/sate-tools-linux/hmmbuild' => '/usr/local/bin/pasta/bin/hmmbuild'
Creating link: '/usr/local/bin/sate-tools-linux/contralign.params' => '/usr/local/bin/pasta/bin/contralign.params'
Creating link: '/usr/local/bin/sate-tools-linux/probcons' => '/usr/local/bin/pasta/bin/probcons'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/bin/mafft' => '/usr/local/bin/pasta/bin/mafftdir/bin/mafft'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/splittbfast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/splittbfast'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/setcore' => '/usr/local/bin/pasta/bin/mafftdir/libexec/setcore'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndpre2' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndpre2'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/pairash' => '/usr/local/bin/pasta/bin/mafftdir/libexec/pairash'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndfast7' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndfast7'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/contrafoldwrap' => '/usr/local/bin/pasta/bin/mafftdir/libexec/contrafoldwrap'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/score' => '/usr/local/bin/pasta/bin/mafftdir/libexec/score'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/getlag' => '/usr/local/bin/pasta/bin/mafftdir/libexec/getlag'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/addsingle' => '/usr/local/bin/pasta/bin/mafftdir/libexec/addsingle'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft-distance' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft-distance'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/restoreu' => '/usr/local/bin/pasta/bin/mafftdir/libexec/restoreu'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/sextet5' => '/usr/local/bin/pasta/bin/mafftdir/libexec/sextet5'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/version' => '/usr/local/bin/pasta/bin/mafftdir/libexec/version'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/makedirectionlist' => '/usr/local/bin/pasta/bin/mafftdir/libexec/makedirectionlist'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/regtable2seq' => '/usr/local/bin/pasta/bin/mafftdir/libexec/regtable2seq'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft.1' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft.1'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/setdirection' => '/usr/local/bin/pasta/bin/mafftdir/libexec/setdirection'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/rnatest' => '/usr/local/bin/pasta/bin/mafftdir/libexec/rnatest'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndblast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndblast'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/seq2regtable' => '/usr/local/bin/pasta/bin/mafftdir/libexec/seq2regtable'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/replaceu' => '/usr/local/bin/pasta/bin/mafftdir/libexec/replaceu'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dndpre' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dndpre'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/dvtditr' => '/usr/local/bin/pasta/bin/mafftdir/libexec/dvtditr'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/pairlocalalign' => '/usr/local/bin/pasta/bin/mafftdir/libexec/pairlocalalign'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft-profile' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft-profile'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/multi2hat3s' => '/usr/local/bin/pasta/bin/mafftdir/libexec/multi2hat3s'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/pair2hat3s' => '/usr/local/bin/pasta/bin/mafftdir/libexec/pair2hat3s'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/tbfast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/tbfast'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafft-homologs.1' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafft-homologs.1'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mafftash_premafft.pl' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mafftash_premafft.pl'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/mccaskillwrap' => '/usr/local/bin/pasta/bin/mafftdir/libexec/mccaskillwrap'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/f2cl' => '/usr/local/bin/pasta/bin/mafftdir/libexec/f2cl'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/countlen' => '/usr/local/bin/pasta/bin/mafftdir/libexec/countlen'
Creating link: '/usr/local/bin/sate-tools-linux/mafftdir/libexec/disttbfast' => '/usr/local/bin/pasta/bin/mafftdir/libexec/disttbfast'
Traceback (most recent call last):
  File "setup.py", line 199, in <module>
    for files in os.listdir(searchDir):
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/bin/sate-tools-linux/databases'

I checked the sate-tools-linux repository, and there's no databases folder, which is why this error is getting triggered. Looking at the commit history, it seems like the files in the databases folder were deleted 11 days ago. I'm not sure what these databases were used for nor how their deletion affects PASTA setup, so I won't remove these symlink lines, but someone should look into this

@niemasd
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niemasd commented Apr 15, 2018

I got around the sate-tools-linux symlink error for now by reverting it to commit d78ef029b533e4f4ac13ba1e9cfdac7944b1f70e before running setup.py

@smirarab
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smirarab commented Apr 15, 2018 via email

@smirarab
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smirarab commented Apr 15, 2018 via email

@niemasd niemasd mentioned this issue Apr 15, 2018
Merged
@zhangwenting0816
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after i type 'sudo python setup.py develop'
i got notes like these：

Creating link: '/home/bin/pasta-code/pasta/resources/scripts/hmmeralign' => '/home/bin/pasta-code/pasta/bin/hmmeralign'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/raxml' => '/home/bin/pasta-code/pasta/bin/raxml'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafft' => '/home/bin/pasta-code/pasta/bin/mafft'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/hmmbuild' => '/home/bin/pasta-code/pasta/bin/hmmbuild'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/hmmalign' => '/home/bin/pasta-code/pasta/bin/hmmalign'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/contralign.topology' => '/home/bin/pasta-code/pasta/bin/contralign.topology'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/contralign.params' => '/home/bin/pasta-code/pasta/bin/contralign.params'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/probcons' => '/home/bin/pasta-code/pasta/bin/probcons'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/opal.jar' => '/home/bin/pasta-code/pasta/bin/opal.jar'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/fasttreeMP' => '/home/bin/pasta-code/pasta/bin/fasttreeMP'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/raxmlp' => '/home/bin/pasta-code/pasta/bin/raxmlp'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/homologs' => '/home/bin/pasta-code/pasta/bin/homologs'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/clustalw2' => '/home/bin/pasta-code/pasta/bin/clustalw2'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/.gitignore' => '/home/bin/pasta-code/pasta/bin/.gitignore'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/fasttree' => '/home/bin/pasta-code/pasta/bin/fasttree'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/fakealigner' => '/home/bin/pasta-code/pasta/bin/fakealigner'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/faketree' => '/home/bin/pasta-code/pasta/bin/faketree'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/contralign' => '/home/bin/pasta-code/pasta/bin/contralign'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/padaligner' => '/home/bin/pasta-code/pasta/bin/padaligner'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/muscle' => '/home/bin/pasta-code/pasta/bin/muscle'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/prank' => '/home/bin/pasta-code/pasta/bin/prank'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/randtree' => '/home/bin/pasta-code/pasta/bin/randtree'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/bin/mafft' => '/home/bin/pasta-code/pasta/bin/mafftdir/bin/mafft'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndpre' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndpre'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/getlag' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/getlag'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/pairlocalalign' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/pairlocalalign'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/makedirectionlist' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/makedirectionlist'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mccaskillwrap' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mccaskillwrap'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/setdirection' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/setdirection'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndblast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndblast'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/contrafoldwrap' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/contrafoldwrap'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/splittbfast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/splittbfast'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/pair2hat3s' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/pair2hat3s'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/f2cl' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/f2cl'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/restoreu' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/restoreu'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/regtable2seq' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/regtable2seq'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/tbfast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/tbfast'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft-distance' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft-distance'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/pairash' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/pairash'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/countlen' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/countlen'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft-homologs.1' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft-homologs.1'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/addsingle' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/addsingle'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/multi2hat3s' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/multi2hat3s'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/replaceu' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/replaceu'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/seq2regtable' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/seq2regtable'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/score' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/score'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/sextet5' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/sextet5'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dvtditr' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dvtditr'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft.1' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft.1'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/disttbfast' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/disttbfast'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafft-profile' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafft-profile'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/setcore' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/setcore'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/mafftash_premafft.pl' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/mafftash_premafft.pl'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/rnatest' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/rnatest'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndfast7' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndfast7'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/dndpre2' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/dndpre2'
Path already exists and is linked correctly.

Creating link: '/home/bin/pasta-code/sate-tools-linux/mafftdir/libexec/version' => '/home/bin/pasta-code/pasta/bin/mafftdir/libexec/version'
Path already exists and is linked correctly.
/usr/local/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'app'
warnings.warn(msg)
running develop
running egg_info
writing PASTA.egg-info/PKG-INFO
writing dependency_links to PASTA.egg-info/dependency_links.txt
writing requirements to PASTA.egg-info/requires.txt
writing top-level names to PASTA.egg-info/top_level.txt
reading manifest file 'PASTA.egg-info/SOURCES.txt'
writing manifest file 'PASTA.egg-info/SOURCES.txt'
running build_ext
Creating /usr/local/lib/python3.6/site-packages/PASTA.egg-link (link to .)
PASTA 1.8.2 is already the active version in easy-install.pth
Installing run_pasta.py script to /usr/local/bin
Installing run_pasta_gui.py script to /usr/local/bin
Installing run_seqtools.py script to /usr/local/bin

Installed /home/bin/pasta-code/pasta
Processing dependencies for PASTA==1.8.2
Searching for dendropy>=4.00
Reading https://pypi.python.org/simple/dendropy/
Downloading https://files.pythonhosted.org/packages/f5/21/17e4fbb1c2a68421eec43930b1e118660c7483229f1b28ba4402e8856884/DendroPy-4.4.0.tar.gz#sha256=f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c

than stop here no continuing
could you help me ?

@smirarab
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smirarab commented Oct 4, 2018 via email

@smirarab
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Niema, was this fixed?

@niemasd
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niemasd commented Jul 17, 2019

I think the DendroPy issue mentioned by zhangwenting0816 is not the same as the issue I had encountered. I believe I fixed my issue in my Docker image by having the Dockerfile use the old commit of the "sate-tools-linux" repository. I don't remember if the master branch of "sate-tools-linux" was ever fixed accordingly or if we ever fixed the master branch of PASTA itself

@antoinekoehl antoinekoehl mentioned this issue Feb 2, 2021
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@smirarab @niemasd @zhangwenting0816