Closed jaipadmakumar closed 3 years ago
I tried installing ISEScan through bioconda one month ago, it works. I posted all my install steps at https://github.com/xiezhq/ISEScan#Bioconda-install. Could you try it step by step?
If you are familiar with Linux, manual install from source should not be a problem for you. However, please try bioconda first to save your time.
Xie
Yea that’s the instruction page I followed and no luck (only difference is I have the full anaconda rather than mini conda).
Are you still able to find it if you just do a conda search for it?
ISEScan bioconda package is still there. The following are the steps I uninstall and re-install it on my centos machine:
[xiezhq@centos7-nat ~]$ conda uninstall isescan
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /apps/inst/miniconda3
removed specs:
- isescan
The following packages will be REMOVED:
biopython-1.76-py37h516909a_0
blast-2.5.0-hc0b0e79_3
boost-1.73.0-py37h429e714_0
boost-cpp-1.73.0-h7b93d67_1
bzip2-1.0.8-h516909a_2
fastcluster-1.1.26-py37h0da4684_1
fraggenescan-1.30-h470a237_2
hmmer-3.3-he1b5a44_1
icu-67.1-he1b5a44_0
isescan-1.7.2.1-h516909a_0
libblas-3.8.0-14_openblas
libcblas-3.8.0-14_openblas
libgfortran-ng-7.5.0-hdf63c60_6
liblapack-3.8.0-14_openblas
libopenblas-0.3.7-h5ec1e0e_6
lz4-c-1.9.2-he1b5a44_1
numpy-1.18.5-py37h8960a57_0
perl-5.26.2-h516909a_1006
scipy-1.4.1-py37ha3d9a3c_3
zstd-1.4.4-h6597ccf_3
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
[xiezhq@centos7-nat ~]$ isescan.py
bash: isescan.py: command not found...
[xiezhq@centos7-nat ~]$ conda install isescan
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /apps/inst/miniconda3
added / updated specs:
- isescan
The following NEW packages will be INSTALLED:
biopython conda-forge/linux-64::biopython-1.76-py37h516909a_0
blast bioconda/linux-64::blast-2.5.0-hc0b0e79_3
boost conda-forge/linux-64::boost-1.73.0-py37h429e714_0
boost-cpp conda-forge/linux-64::boost-cpp-1.73.0-h7b93d67_1
bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2
fastcluster conda-forge/linux-64::fastcluster-1.1.26-py37h0da4684_1
fraggenescan bioconda/linux-64::fraggenescan-1.30-h470a237_2
hmmer bioconda/linux-64::hmmer-3.3-he1b5a44_1
icu conda-forge/linux-64::icu-67.1-he1b5a44_0
isescan bioconda/linux-64::isescan-1.7.2.1-h516909a_0
libblas conda-forge/linux-64::libblas-3.8.0-14_openblas
libcblas conda-forge/linux-64::libcblas-3.8.0-14_openblas
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_6
liblapack conda-forge/linux-64::liblapack-3.8.0-14_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.7-h5ec1e0e_6
lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1
numpy conda-forge/linux-64::numpy-1.18.5-py37h8960a57_0
perl conda-forge/linux-64::perl-5.26.2-h516909a_1006
scipy conda-forge/linux-64::scipy-1.4.1-py37ha3d9a3c_3
zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
[xiezhq@centos7-nat ~]$ isescan.py
usage: isescan [-h] [--version] [--removeShortIS] [--no-FragGeneScan]
[--nthread NTHREAD]
seqfile path2proteome path2hmm
isescan: error: the following arguments are required: seqfile, path2proteome, path2hmm_
Xie
Ok thanks for double checking. Not sure what the issue but here's the full error for the record:
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- isescan
Current channels:
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://conda.anaconda.org/bioconda/osx-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://conda.anaconda.org/bpteague/osx-64
- https://conda.anaconda.org/bpteague/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
This might be a more general problem. It looks like there are others with a similar issue on other packages (https://github.com/conda/conda/issues/9653). Anyways, thanks for the help!
You can try installing isescan in conda-forge or bioconda channel. The following is my test.
conda create -m -p test/isescan
source activate /home2/s178588/test/isescan
conda install -c conda-forge isescan
test/isescan/bin/isescan.py
Good luck! Xie
Hey, I still run into exactly the same problem: "PackagesNotFoundError" on mac.
Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
Current channels:
To search for alternate channels that may provide the conda package you're looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Whereas when I try to install from the source its impossible to install FragGeneScan.. :/
Hi Anna Gorska,
I have no idea about ISEScan on mac as I only fully tested it on Linux. I knew there is compling issue for FragGensScan on Mac but I once solved it. To solve the problem of running FragGeneScan on Mac, please modify two source files in FragGeneScan source codes: 1) open util_lib.c and comment out ‘#include
Hope it helps!
Xie
From: Anna Górska notifications@github.com Sent: Wednesday, September 16, 2020 5:35 AM To: xiezhq/ISEScan ISEScan@noreply.github.com Cc: Zhiqun Xie Zhiqun.Xie@UTSouthwestern.edu; State change state_change@noreply.github.com Subject: Re: [xiezhq/ISEScan] ISEScan not available through Bioconda? (#20)
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Hey, I still run into exactly the same problem: "PackagesNotFoundError" on mac.
Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
Current channels:
To search for alternate channels that may provide the conda package you're looking for, navigate to
and use the search bar at the top of the page.
Whereas when I try to install from the source its impossible to install FragGeneScan.. :/
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Dear Xie,
thanks a lot for your reply. I have solved it around, just by installing on my linux box (which took 30s and run without issues). I think it would be useful to put some note about possible Mac-problems, cause I spent some hours trying to hunt down this error,
regards, Anna
Thank you for the good suggestion, Anna. I will find time to write a FAQ list including the Mac-problem you mentioned.
Best, Xie
Update, a section ISEScan on mac
was added in Installation
to provide hints for compiling FragGensScan codes on Mac.
I'm not sure if this should be posted here or on the Bioconda page but I can't seem to locate the package through Conda. I get a
PackagesNotFoundError
when I try to install withconda install -c bioconda isescan
. Is this a known issue and, if so, should I just go ahead with a manual install?