Closed arturomarin closed 5 years ago
Hi there,
I'm not immediately sure what the problem could be but it could be worth it to try installing the package using pip.
If you're in the HyDe/
directory that was cloned from GitHub, try running this command:
pip install -U .
Hi,
the command does not work:
[root@DESEBDDOCKER01 HyDe]# pip install -U
ERROR: You must give at least one requirement to install (see "pip help install")
Is there something missing in the command?
It's kind of hard to see, but the command should have a dot, .
, after the pip install -U
. This tells pip
to build the package in the current directory.
pip install -U .
Thanks. Now I have another error:
[root@DESEBDDOCKER01 HyDe]# pip install -U .
Processing /root/HyDe
Complete output from command python setup.py egg_info:
ERROR:
You are missing the following required modules:
seaborn
ERROR:
Unable to install phyde.
Please see the documentation at http://hybridization-detection.rtfd.io/.
----------------------------------------
Command "python setup.py egg_info" failed with error code 255 in /tmp/pip-req-build-P9Eb4f/
[root@DESEBDDOCKER01 HyDe]#
Is somethog stranger because seaborn is installed
[root@DESEBDDOCKER01 ~]# pip install seaborn
Requirement already satisfied: seaborn in /usr/lib/python2.7/site-packages (0.9.0)
Requirement already satisfied: numpy>=1.9.3 in /usr/lib64/python2.7/site-packages (from seaborn) (1.15.2)
Requirement already satisfied: scipy>=0.14.0 in /usr/lib64/python2.7/site-packages (from seaborn) (1.1.0)
Requirement already satisfied: pandas>=0.15.2 in /usr/lib64/python2.7/site-packages (from seaborn) (0.23.4)
Requirement already satisfied: matplotlib>=1.4.3 in /usr/lib64/python2.7/site-packages (from seaborn) (2.2.3)
Requirement already satisfied: pytz>=2011k in /usr/lib/python2.7/site-packages (from pandas>=0.15.2->seaborn) (2018.5)
Requirement already satisfied: python-dateutil>=2.5.0 in /usr/lib/python2.7/site-packages (from pandas>=0.15.2->seaborn) (2.7.3)
Requirement already satisfied: subprocess32 in /usr/lib64/python2.7/site-packages (from matplotlib>=1.4.3->seaborn) (3.5.2)
Requirement already satisfied: cycler>=0.10 in /usr/lib/python2.7/site-packages (from matplotlib>=1.4.3->seaborn) (0.10.0)
Requirement already satisfied: six>=1.10 in /usr/lib/python2.7/site-packages (from matplotlib>=1.4.3->seaborn) (1.11.0)
Requirement already satisfied: backports.functools-lru-cache in /usr/lib/python2.7/site-packages (from matplotlib>=1.4.3->seaborn) (1.5)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/lib/python2.7/site-packages (from matplotlib>=1.4.3->seaborn) (2.2.2)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/lib64/python2.7/site-packages (from matplotlib>=1.4.3->seaborn) (1.0.1)
Requirement already satisfied: setuptools in /usr/lib/python2.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=1.4.3->seaborn) (40.4.3)
[root@DESEBDDOCKER01 ~]#
Ok, so it looks like there is some miscommunication between where the packages are installed and where Python is looking for them. It looks like you are using Docker, so I went ahead and built a Docker image that should hopefully have everything installed correctly. The code below should get you started.
# 1. Pull the hyde-docker image
docker pull pblischak/hyde-docker
# 2. Run the image and connect the folder with you data so that you can analyze it
docker run -it -v </path/to/your/data>:/home pblischak/hyde-docker
Make sure you substitute </path/to/your/data/>
with the actual path (and make sure the greater than and less than symbols are removed too). After that, you should be able to run the run_hyde.py
script like in the documentation.
I apologize for the delay in answering. We had problems with the server hardware and had to stop installing programs on the server. You can close the issue, and if I try again to install the program and I have problems I will post an issue.
No worries! I'm happy to help if need be
Hi,
I can install HyDe using the guide, but when I try the test whith make test it give me an error:
thanks in advance