I am running whole genome sequencing analysis on a number of samples and I am using Conda to install sickle (version 0.7.0). The package does not seem to be found despite that it was successfully installed.
Here are the steps I followed:
installed Miniconda3 (version 4.14.0) and created an environment using
conda env create -n package.activated conda environment using
conda activate packageinstalled sickle with required version 0.7.0 using
conda install -c bioconda sickle=0.7.0checked whether this was successfully installed using
conda list. This returned:
# packages in environment at /home/miniconda3/envs/package:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
brotlipy 0.7.0 py310h7f8727e_1002
bzip2 1.0.8 h7b6447c_0
ca-certificates 2022.07.19 h06a4308_0
certifi 2022.6.15 py310h06a4308_0
cffi 1.15.1 py310h74dc2b5_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
cryptography 37.0.1 py310h9ce1e76_0
icu 58.2 he6710b0_3
idna 3.3 pyhd3eb1b0_0
ld_impl_linux-64 2.38 h1181459_1
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libstdcxx-ng 11.2.0 h1234567_1
libuuid 1.0.3 h7f8727e_2
libxml2 2.9.14 h74e7548_0
libxslt 1.1.35 h4e12654_0
lxml 4.9.1 py310h1edc446_0
ncurses 6.3 h5eee18b_3
openssl 1.1.1q h7f8727e_0
pip 22.1.2 py310h06a4308_0
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 22.0.0 pyhd3eb1b0_0
pysocks 1.7.1 py310h06a4308_0
python 3.10.4 h12debd9_0
readline 8.1.2 h7f8727e_1
requests 2.28.1 py310h06a4308_0
setuptools 63.4.1 py310h06a4308_0
sickle 0.7.0 pyh9f0ad1d_0 bioconda
sqlite 3.39.2 h5082296_0
tk 8.6.12 h1ccaba5_0
tzdata 2022a hda174b7_0
urllib3 1.26.11 py310h06a4308_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.5 h7f8727e_1
zlib 1.2.12 h7f8727e_2
- tried to call
sickleon command line:
$ sickle --help
Command 'sickle' not found, but can be installed with:
apt install sickle
Please ask your administrator.
Would someone please assist me or let me know what I am doing wrong?