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snayfach / MIDAS

An integrated pipeline for estimating strain-level genomic variation from metagenomic data
http://dx.doi.org/10.1101/gr.201863.115
GNU General Public License v3.0
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How to check which version of MIDAS is running? #97

Open jolespin opened 5 years ago

jolespin commented 5 years ago

I finally got a (semi) clean version of MIDAS running in my MIDAS-specific conda environment. However, I installed using both pip and conda. I'm not sure which one is actually being used and I'm afraid to break the environment but I would like to clean it up so I can make a manual on how to install for my coworkers.

Just to be clear, MIDAS now works with python3? 

(midas_env) -bash-4.1$ conda list
# packages in environment at /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/midas_env:
#
# Name                    Version                   Build  Channel
bcftools                  1.9                  h47928c2_2    bioconda
biopython                 1.68                     py35_0    bioconda
blas                      1.0                         mkl
blast                     2.5.0                hc0b0e79_3    bioconda
boost                     1.67.0                   py35_4
bowtie2                   2.3.4.3          py35h2d50403_0    bioconda
bzip2                     1.0.6                h14c3975_5
ca-certificates           2019.1.23                     0
certifi                   2018.8.24                py35_1
curl                      7.61.0               h84994c4_0
cython                    0.28.5           py35hf484d3e_0
freetype                  2.9.1                h8a8886c_1
hs-blastn                 0.0.5                h470a237_1    bioconda
htslib                    1.9                  h47928c2_5    bioconda
icu                       58.2                 h9c2bf20_1
intel-openmp              2019.1                      144
jpeg                      9b                   h024ee3a_2
libboost                  1.67.0               h46d08c1_4
libcurl                   7.61.0               h1ad7b7a_0
libdeflate                1.0                  h14c3975_1    bioconda
libedit                   3.1.20181209         hc058e9b_0
libffi                    3.2.1                hd88cf55_4
libgcc-ng                 8.2.0                hdf63c60_1
libgfortran-ng            7.3.0                hdf63c60_0
libpng                    1.6.36               hbc83047_0
libssh2                   1.8.0                h9cfc8f7_4
libstdcxx-ng              8.2.0                hdf63c60_1
libtiff                   4.0.10               h2733197_2
midas                     1.3.2            py35h24bf2e0_2    bioconda
MIDAS                     1.3.0                     <pip>
mkl                       2018.0.3                      1
mkl_fft                   1.0.6            py35h7dd41cf_0
mkl_random                1.0.1            py35h4414c95_1
mmtf-python               1.0.2                    py35_0    bioconda
msgpack-python            0.5.6            py35h6bb024c_1
ncurses                   6.1                  he6710b0_1
numpy                     1.15.2           py35h1d66e8a_0
numpy-base                1.15.2           py35h81de0dd_0
olefile                   0.46                     py35_0
openssl                   1.0.2r               h7b6447c_0
pandas                    0.23.4           py35h04863e7_0
perl                      5.26.2               h14c3975_0
pillow                    5.2.0            py35heded4f4_0
pip                       10.0.1                   py35_0
py-boost                  1.67.0           py35h04863e7_4
pymodbus                  2.2.0rc1                  <pip>
pysam                     0.15.2           py35h0380709_0    bioconda
pyserial                  3.4                       <pip>
python                    3.5.6                hc3d631a_0
python-dateutil           2.7.3                    py35_0
pytz                      2018.5                   py35_0
readline                  7.0                  h7b6447c_5
reportlab                 3.5.6            py35he686d34_0
samtools                  1.9                  h57cc563_6    bioconda
setuptools                40.2.0                   py35_0
six                       1.11.0                   py35_1
sqlite                    3.26.0               h7b6447c_0
tk                        8.6.8                hbc83047_0
wheel                     0.31.1                   py35_0
xz                        5.2.4                h14c3975_4
zlib                      1.2.11               h7b6447c_3
zstd                      1.3.7                h0b5b093_0