Closed joqb closed 4 years ago
Hi @eaton-lab,
I want to run tetrad but it keeps asking for toytree although I just installed it... What versions do you recommend? Thanks
(base) [ghanavati@bit-10 for-fastq]$ tetrad -s /filer-5/user/ghanavati/for-fastq/datatest_outfiles/datatest.snps.phy -l /filer-5/user/ghanavati/for-fastq/datatest_outfiles/datatest.snps.map -n 189chamomile -o /filer-5/user/ghanavati/for-fastq/ -c 10 -b 100 - random -q 1000000 Traceback (most recent call last): File "/filer-5/user/ghanavati/miniconda2/bin/tetrad", line 11, in <module> load_entry_point('ipyrad==0.7.30', 'console_scripts', 'tetrad')() File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2843, in load_entry_point return ep.load() File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2434, in load return self.resolve() File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2440, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/__init__.py", line 18, in <module> from .structure import Structure as structure File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/structure.py", line 12, in <module> from ipyrad.analysis.tetrad import get_spans File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/tetrad.py", line 67, in <module> """) File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.py", line 52, in __init__ raise IPyradError(*args, **kwargs) ipyrad.assemble.util.IPyradError: Error: tetrad requires the dependency 'toytree', which we haven't yet included in the ipyrad installation. For now, you can install toytree using conda with the following command: conda install toytree -c eaton-lab (base) [ghanavati@bit-10 for-fastq]$ conda install toytree -c eaton-lab Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /filer-5/user/ghanavati/miniconda2 added / updated specs: - toytree The following packages will be downloaded: package | build ---------------------------|----------------- arrow-0.13.1 | py27_0 83 KB custom_inherit-2.2.0 | py27_0 30 KB eaton-lab ghostscript-9.21 | 0 4 KB eaton-lab multipledispatch-0.6.0 | py27_0 21 KB pypng-0.0.18 | py27_0 81 KB eaton-lab reportlab-3.5.23 | py27he686d34_0 2.2 MB toyplot-0.18.0 | py27_0 342 KB eaton-lab toytree-0.2.0 | py27_1 151 KB eaton-lab ------------------------------------------------------------ Total: 2.9 MB The following NEW packages will be INSTALLED: arrow pkgs/main/linux-64::arrow-0.13.1-py27_0 custom_inherit eaton-lab/linux-64::custom_inherit-2.2.0-py27_0 ghostscript eaton-lab/linux-64::ghostscript-9.21-0 multipledispatch pkgs/main/linux-64::multipledispatch-0.6.0-py27_0 pypng eaton-lab/linux-64::pypng-0.0.18-py27_0 reportlab pkgs/main/linux-64::reportlab-3.5.23-py27he686d34_0 toyplot eaton-lab/linux-64::toyplot-0.18.0-py27_0 toytree eaton-lab/linux-64::toytree-0.2.0-py27_1 Proceed ([y]/n)? Downloading and Extracting Packages pypng-0.0.18 | 81 KB | ######################################################################## | 100% toytree-0.2.0 | 151 KB | ######################################################################## | 100% ghostscript-9.21 | 4 KB | ######################################################################## | 100% arrow-0.13.1 | 83 KB | ######################################################################## | 100% custom_inherit-2.2.0 | 30 KB | ######################################################################## | 100% toyplot-0.18.0 | 342 KB | ######################################################################## | 100% multipledispatch-0.6 | 21 KB | ######################################################################## | 100% reportlab-3.5.23 | 2.2 MB | ######################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (base) [ghanavati@bit-10 for-fastq]$ tetrad -s /filer-5/user/ghanavati/for-fastq/datatest_outfiles/datatest.snps.phy -l /filer-5/user/ghanavati/for-fastq/datatest_outfiles/datatest.snps.map -n 189chamomile -o /filer-5/user/ghanavati/for-fastq/ -c 10 -b 100 - random -q 1000000 Traceback (most recent call last): File "/filer-5/user/ghanavati/miniconda2/bin/tetrad", line 11, in <module> load_entry_point('ipyrad==0.7.30', 'console_scripts', 'tetrad')() File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2843, in load_entry_point return ep.load() File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2434, in load return self.resolve() File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2440, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/__init__.py", line 18, in <module> from .structure import Structure as structure File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/structure.py", line 12, in <module> from ipyrad.analysis.tetrad import get_spans File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/tetrad.py", line 67, in <module> """) File "/filer-5/user/ghanavati/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.py", line 52, in __init__ raise IPyradError(*args, **kwargs) ipyrad.assemble.util.IPyradError: Error: tetrad requires the dependency 'toytree', which we haven't yet included in the ipyrad installation. For now, you can install toytree using conda with the following command: conda install toytree -c eaton-lab (base) [ghanavati@bit-10 miniconda2]$ conda install toytree -c eaton-lab Collecting package metadata (current_repodata.json): done Solving environment: done # All requested packages already installed.
This is now fixed, note the new conda install command:
conda install tetrad -c eaton-lab -c conda-forge
Hi @eaton-lab,
I want to run tetrad but it keeps asking for toytree although I just installed it... What versions do you recommend? Thanks