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sickle not found though installed.

Open skr3178 opened this issue 2 years ago • 0 comments

Command 'sickle' not found, but can be installed with: sudo apt install sickle

Here is my env:

var3) ubuntu@ip-172-31-20-167:~$ mamba list
# packages in environment at /home/ubuntu/miniconda3/envs/var3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bcftools                  1.9                  h68d8f2e_9    bioconda
biopython                 1.70                np112py35_1    bioconda
blas                      1.1                    openblas    conda-forge
bwa                       0.7.17               h7132678_9    bioconda
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2022.9.24            ha878542_0    conda-forge
certifi                   2018.8.24             py35_1001    conda-forge
curl                      7.64.0               h646f8bb_0    conda-forge
freetype                  2.12.1               hca18f0e_0    conda-forge
gsl                       2.5                  h294904e_1    conda-forge
htslib                    1.9                  ha228f0b_7    bioconda
icu                       70.1                 h27087fc_0    conda-forge
jpeg                      9e                   h166bdaf_2    conda-forge
krb5                      1.16.3            hc83ff2d_1000    conda-forge
libblas                   3.9.0           1_h86c2bf4_netlib    conda-forge
libcblas                  3.9.0           5_h92ddd45_netlib    conda-forge
libcurl                   7.64.0               h01ee5af_0    conda-forge
libdeflate                1.0                  h14c3975_1    bioconda
libedit                   3.1.20191231         h46ee950_2    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libpng                    1.6.38               h753d276_0    conda-forge
libssh2                   1.8.0             h1ad7b7a_1003    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtiff                   4.2.0                hf544144_3    conda-forge
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libxml2                   2.10.3               h7463322_0    conda-forge
libxslt                   1.1.37               h873f0b0_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
lxml                      4.2.5            py35hc9114bc_0    conda-forge
mmtf-python               1.0.2                    py35_0    bioconda
msgpack-python            0.5.6            py35h2d50403_3    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
numpy                     1.12.1          py35_blas_openblas_201    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openblas                  0.2.20                        8    conda-forge
openssl                   1.0.2u               h516909a_0    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pillow                    5.3.0            py35hc736899_0    conda-forge
pip                       20.3.4             pyhd8ed1ab_0    conda-forge
python                    3.5.5                h5001a0f_2    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
reportlab                 3.5.8            py35h77bcf2c_0    conda-forge
requests                  2.13.0                   py35_0    conda-forge
samtools                  1.9                 h10a08f8_12    bioconda
setuptools                40.4.3                   py35_0    conda-forge
sickle                    0.7.0              pyh9f0ad1d_0    bioconda
sqlite                    3.28.0               h8b20d00_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.2                h6239696_4    conda-forge
(var3) ubuntu@ip-172-31-20-167:~$ mamba lsickle
No command 'conda lsickle'.

skr3178 avatar Nov 10 '22 02:11 skr3178