HyDe is installed while make test does not worked

[Yung-Chien]

Hi @pblischak ,
I've finished the installation work of HyDe, but I got some error when I typed 'make test', the result as below,

`**** Testing run_hyde.py (full analysis). ****
run_hyde.py -i examples/snake-data.txt -m examples/snake-map.txt -n 52 -t 7 -s 8466 -o out

Traceback (most recent call last):
File "/home1/xxx/miniconda2/envs/geno/bin/run_hyde.py", line 4, in
import('pkg_resources').run_script('phyde==0.4.3', 'run_hyde.py')

File "/home1/xxx/miniconda2/envs/geno/lib/python3.6/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)

File "/home1/xxx/miniconda2/envs/geno/lib/python3.6/site-packages/pkg_resources/init.py", line 1453, in run_script
.format(**locals()),

pkg_resources.ResolutionError: Script 'scripts/run_hyde.py' not found in metadata at '/home1/xxx/software/HyDe/phyde.egg-info'
make: *** [Makefile:7: test] Error 1
`
So how could I fix this problem, or does this issue have any effect of following analyzation of HyDe?
Thanks in advances，
Yung-Chien

[pblischak]

Hi @Yung-Chien ,

This looks like a PATH error for the environment that you are using with Miniconda2. Did you install HyDe while the geno envorinment was active? Also, from the last bit, it looks like your computer is looking for the HyDe scripts in /home1/xxx/software/HyDe. How/where exactly did you install everything?

[Yung-Chien]

Hi @pblischak ,

Yes I installed HyDe when the geno envorinment was active, And definitely I compile and install the source at /home1/xxx/software/HyDe. However, I tried to reinstall HyDe in the base environment with a 2.7 version Python, it had the same error. More strangely, When I entered the script directory and type

python run_hyde.py -h

I got this,
`usage: run_hyde.py [-h] -i -m -o -n -t -s [-tr] [-p]
[--prefix] [-q] [--ignore_amb_sites]

Options for run_hyde.py

optional arguments:
-h, --help show this help message and exit

required arguments:
-i, --infile name of the data input file
-m, --map map of individuals to taxa
-o, --outgroup name of the outgroup (only one accepted)
-n, --num_ind number of individuals in data matrix
-t, --num_taxa number of taxa (species, OTUs)
-s, --num_sites number of sites in the data matrix

additional arguments:
-tr, --triples table of triples to be analyzed
-p, --pvalue p-value cutoff for test of significance [default=0.05]
--prefix prefix appended to output files [default=hyde]
-q, --quiet supress printing to stdout
--ignore_amb_sites ignore missing/ambiguous sites
`

It seemed like a right output, so I was still confused about what kind of problems I got in the progress of installation. Thank you for answering my question.
Yung-Chien

[snehasjoshi]

Hi Yung-Chien
I am encountering the same problem. Can you please let me know how did you solve this?