search

donovan-h-parks / STAMP

Statistical Analysis of Metagenomic Profiles
GNU General Public License v3.0
91 stars 35 forks source link

installing STAMP on macOS #34

Open fconstancias opened 4 years ago

fconstancias commented 4 years ago

Dear All,

I am also having troubles install STAMP on macOS. It seems that Python 2.7 reached the end of its life on January 1st, 2020 thus we can not install stamp anymore on macOS?

I have tried both :

conda create python=2.7 -y -n stamp 
pip install numpy
pip install STAMP
pip install cython
pip install STAMP

and got the following error

[1/3] Cythonizing biom/_filter.pyx
[2/3] Cythonizing biom/_subsample.pyx
[3/3] Cythonizing biom/_transform.pyx
Python 2.7 is no longer supported
----------------------------------------

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

or :

conda create python=2.7 -y -n stamp 
conda activate stamp
conda install -c bioconda stamp

and got the following error

Package pip conflicts for: python=2.7 -> pip Package libffi conflicts for: python=2.7 -> libffi[version='3.2.|>=3.2.1,<3.3.0a0|>=3.2.1,<4.0a0'] Package scipy conflicts for: stamp -> scipy[version='>=0.15.1'] Package pyqi conflicts for: stamp -> pyqi[version='>=0.3.2'] Package sqlite conflicts for: python=2.7 -> sqlite[version='3.13.|3.20.|>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.28.0,<4.0a0|>=3.29.0,<4.0a0|>=3.30.0,<4.0a0'] Package pyqt conflicts for: stamp -> pyqt[version='4.|>=4.11.4,<4.12.0a0'] Package matplotlib conflicts for: stamp -> matplotlib[version='>=1.4.2'] Package ca-certificates conflicts for: python=2.7 -> ca-certificates Package ncurses conflicts for: python=2.7 -> ncurses[version='>=6.0,<7.0a0|>=6.1,<7.0a0'] Package numpy conflicts for: stamp -> numpy[version='>=1.9.1'] Package six conflicts for: stamp -> six[version='>=1.3'] Package openssl conflicts for: python=2.7 -> openssl[version='1.0.|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a'] Package libcxx conflicts for: python=2.7 -> libcxx[version='>=4.0.1'] Package biom-format conflicts for: stamp -> biom-format[version='>=2.0.1'] Package readline conflicts for: python=2.7 -> readline[version='6.2.|7.|7.0.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0'] Package tk conflicts for: python=2.7 -> tk[version='8.5.|8.6.|>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.9,<8.7.0a0'] Package zlib conflicts for: python=2.7 -> zlib[version='1.2.|1.2.11.|1.2.11|1.2.8|>=1.2.11,<1.3.0a0']

Any help would be much appreciated.

Best.

Florentin

ZhangDengwei commented 4 years ago

I will advise you to use conda with python 2.7 to install STAMP. Please see the following code to install step by step.

conda install -n root conda=4.6
conda create -n stamp
conda activate stamp
conda install -y -c bioconda stamp
STAMP
DPC7 commented 4 years ago

Hi @fconstancias have you installed STAMP? I am new in this field and also very recently I have installed STAMP. But I am getting the following error:

Error reading profile file
 Child g__Gemella has an unclassified parent.

Many taxa are in the abundance file (Metaphlan 3.0) for which an unclassified parent level taxa is present. Do you have any solution to that? One more query: Is it possible to import metaphlan merged abundance file in "Curatedmetagenomic data" package and then follow the pipeline for statistical analysis?

hernaizjc commented 3 years ago

I will advise you to use conda with python 2.7 to install STAMP. Please see the following code to install step by step.

conda install -n root conda=4.6
conda create -n stamp
conda activate stamp
conda install -y -c bioconda stamp
STAMP

I have the same issue installing STAMP. I created a conda environment that uses python 2.7, but I still get the same results. Any suggestions?

diegoibt commented 3 years ago

I have the same issue installing STAMP on MacOS 10.14.6 Mojave. I created a conda environment that uses python 2.7, but I still get the same results. Any suggestions?

ditag commented 3 years ago

I will advise you to use conda with python 2.7 to install STAMP. Please see the following code to install step by step.

conda install -n root conda=4.6
conda create -n stamp
conda activate stamp
conda install -y -c bioconda stamp
STAMP

For those, who are failing to install STAMP on MacOS - with the above-mentioned commands I was able to install it on my macOS Catalina (v.10.15.7), but somehow software refuses to upload my dataset.. 🤦

mf0083 commented 3 years ago

I am having a similar issue. I followed the following instructions on a help forum

"Someone in my lab helped me fix this issue. It had to with the current biom-format in python not supporting python 2.7. You therefore need to install an older version. Hope this helps conda create -n stamp python=2.7 conda activate stamp pip install numpy pip install cython pip install biom-format==2.1.7 pip install STAMP conda install -n stamp -c asmeurer pyqt=4 STAMP "

However, when I get to the final step of entering STAMP, I get an error that says no module named PyQt4. I have tried several methods of installing PyQt4 (e.g., conda install pyqt=4). I am using python 2.7, and here are the versions of the other packages given by pip list: backports.functools-lru-cache 1.6.4 biom-format 2.1.7 click 7.1.2 cycler 0.10.0 Cython 0.29.23 future 0.18.2 kiwisolver 1.1.0 matplotlib 2.2.5 numpy 1.16.6 pandas 0.24.2 pip 20.3.4 pyparsing 2.4.7 pyqi 0.3.2 python-dateutil 2.8.1 python-qt 0.50 pytz 2021.1 scipy 1.2.3 setuptools 44.1.1 six 1.16.0 STAMP 2.1.3 subprocess32 3.5.4 wheel 0.36.2

Anyone have any suggestions?

Malytherin commented 3 years ago

Hi all,

If you are still having issues, I had success running the following code to install STAMP on my MacOS Big Sur using conda 4.9. The code is the same as above except I added the python=2.7. It seems you need to create an environment with an older version of python since newer versions do not support STAMP (as far as I could tell). Hope this helps!

conda create -n stamp python=2.7
conda activate stamp
conda install -y -c bioconda stamp
STAMP
mf0083 commented 3 years ago

Hi all,

If you are still having issues, I had success running the following code to install STAMP on my MacOS Big Sur using conda 4.9. The code is the same as above except I added the python=2.7. It seems you need to create an environment with an older version of python since newer versions do not support STAMP (as far as I could tell). Hope this helps!

conda create -n stamp python=2.7 conda activate stamp conda install -y -c bioconda stamp STAMP

Hey, thanks for replying! I still get this error even when I specify python=2.7

_UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

Your python: python=2.7_

Hiromori827 commented 3 years ago

Hi Dear

I am also having troubles install STAMP on macOS. I did the above command, but I got the following error message. Which python version should I use?

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

  • stamp -> python[version='3.4.|3.5.|3.6.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0']

Your python: python=2.7

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

cortegas commented 2 years ago

Hello everyone,

The issue was posted 2 years ago and I see that there is no solution for it. Does anyone who is on the comment chain actually find the solution to install STAMP on MacOS? I am having exactly the same problem as @Hiromori827 @mf0083

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

Your python: python=2.7

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

Any help is highly appreciated it!

Thank you

yonghyun09 commented 1 year ago

After confirming that other solution answers have not been uploaded after the issue conversation above, I will write an additional one.   The reason why the following error message appears after installing and activating stamp with python=2.7 is that other packages necessary for running stamp in the Python environment are not set.

stamp -> python[version='3.4.|3.5.|3.6.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0']

You will need to pre-install the following packages as stated on the stamp installation instructions page.

Therefore, I succeeded in installing the stamp through the code below.

conda create -n stamp python=2.7

conda activate stamp

pip install matplotlib==1.4.2

pip install numpy

pip install cython

pip install biom-format==2.1.7

pip install STAMP

conda install -n stamp -c asmeurer pyqt=4

STAMP

Hope this helps others.

miriamgallardo commented 11 months ago

Hello! I have tried all the codes you all have submitted here in the comments, yet this is what I get when I try to install STAMP on my Big Sur 11.7.10

Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

Could not solve for environment specs The following packages are incompatible └─ stamp is not installable because there are no viable options ├─ stamp 2.1.3 would require │ └─ pyqt 4.* , which does not exist (perhaps a missing channel); └─ stamp 2.1.3 would require └─ pyqt >=4.11.4,<4.12.0a0 , which does not exist (perhaps a missing channel).

I have also found this issue when I have tried to install the packages mentioned in the last comment:

DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support

Any ideas?