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Chow Castro, Marcos
cami
Commits
0918f09c
Commit
0918f09c
authored
Feb 27, 2023
by
Le, Mia
Browse files
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Plain Diff
updated CAMI installation steps
parent
2826bba6
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Changes
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2 changed files
cami.sh
+2
-3
2 additions, 3 deletions
cami.sh
cami_env.yaml
+10
-255
10 additions, 255 deletions
cami_env.yaml
with
12 additions
and
258 deletions
cami.sh
+
2
−
3
View file @
0918f09c
...
...
@@ -70,7 +70,6 @@ END
}
menu
()
{
clear
echo
"===================================="
echo
"| CAMI ENVIRONMENT INSTALLER |"
echo
"|----------------------------------|"
...
...
@@ -97,7 +96,7 @@ install_cami() {
conda config
--add
channels conda-forge
conda config
--add
channels bioconda
echo
"cami: creating environment variable with python 3.7"
conda create
-
-name
cami
-c
conda-forge graph-tool
python
=
3.7
conda
env
create
-
f
cami_env.yaml
echo
"======================================="
echo
"| CAMI ENV SUCCESSFULLY CREATED |"
echo
"|-------------------------------------|"
...
...
@@ -178,7 +177,7 @@ case $cami_tmp in
h|H
)
usage
;;
c|C
)
copyright
;;
a|A
)
conda activate cami
||
echo
"cami: If it was not activated successfully, please try manually: conda activate cami"
;;
u|U
)
conda
install
numpy matplotlib pandas networkx pip jupyter
requests
;
pip
install
pcst_fast
;
conda
env
update cami
--file
=
cami_env.yaml
;;
u|U
)
conda
env
update cami
--file
=
cami_env.yaml
;
pip
install
domino-python
;
pip
install
requests
_html
;
pip
install
biodigest
;;
d|D
)
conda deactivate
;;
s|S
)
conda info
--envs
;;
r|R
)
remove_cami
;;
...
...
This diff is collapsed.
Click to expand it.
cami_env.yaml
+
10
−
255
View file @
0918f09c
...
...
@@ -4,258 +4,13 @@ channels:
-
conda-forge
-
defaults
dependencies
:
-
appnope=0.1.2
-
argcomplete=1.12.3
-
argon2-cffi=21.1.0
-
argon2-cffi-bindings=21.2.0
-
async_generator=1.10
-
atk-1.0=2.36.0
-
attrs=21.2.0
-
backcall=0.2.0
-
backports=1.0
-
backports.functools_lru_cache=1.6.4
-
bleach=4.1.0
-
boost=1.72.0
-
boost-cpp=1.72.0
-
bottleneck=1.3.4
-
brotli=1.0.9
-
brotli-bin=1.0.9
-
brotlipy=0.7.0
-
bzip2=1.0.8
-
c-ares=1.18.1
-
ca-certificates=2021.10.8
-
cached-property=1.5.2
-
cached_property=1.5.2
-
cairo=1.16.0
-
cairomm=1.12.2
-
cairomm-1.0=1.12.2
-
certifi=2021.10.8
-
cffi=1.15.0
-
charset-normalizer=2.0.10
-
cryptography=36.0.0
-
cycler=0.11.0
-
dbus=1.13.6
-
debugpy=1.5.1
-
decorator=5.1.0
-
defusedxml=0.7.1
-
entrypoints=0.3
-
epoxy=1.5.9
-
expat=2.4.1
-
fancycompleter=0.9.1
-
flit-core=3.7.1
-
font-ttf-dejavu-sans-mono=2.37
-
font-ttf-inconsolata=3.000
-
font-ttf-source-code-pro=2.038
-
font-ttf-ubuntu=0.83
-
fontconfig=2.13.1
-
fonts-conda-ecosystem=1
-
fonts-conda-forge=1
-
fonttools=4.28.1
-
freetype=2.10.4
-
fribidi=1.0.10
-
gdk-pixbuf=2.42.6
-
gettext=0.19.8.1
-
giflib=5.2.1
-
glib=2.70.1
-
glib-tools=2.70.1
-
gmp=6.2.1
-
graph-tool=2.35
-
graphite2=1.3.13
-
gtk3=3.24.22
-
h5py=3.6.0
-
harfbuzz=2.4.0
-
hdf5=1.12.1
-
hicolor-icon-theme=0.17
-
icu=64.2
-
idna=3.3
-
importlib-metadata=4.8.2
-
importlib_metadata=4.8.2
-
importlib_resources=5.4.0
-
ipykernel=6.5.0
-
ipython=7.29.0
-
ipython_genutils=0.2.0
-
ipywidgets=7.6.5
-
jbig=2.1
-
jedi=0.18.1
-
jinja2=3.0.3
-
jpeg=9d
-
jsonschema=4.2.1
-
jupyter=1.0.0
-
jupyter_client=7.0.6
-
jupyter_console=6.4.0
-
jupyter_core=4.9.1
-
jupyterlab_pygments=0.1.2
-
jupyterlab_widgets=1.0.2
-
kiwisolver=1.3.2
-
krb5=1.19.2
-
lcms2=2.12
-
lerc=3.0
-
libblas=3.9.0
-
libbrotlicommon=1.0.9
-
libbrotlidec=1.0.9
-
libbrotlienc=1.0.9
-
libcblas=3.9.0
-
libclang=13.0.1
-
libcurl=7.81.0
-
libcxx=12.0.1
-
libdeflate=1.8
-
libedit=3.1.20191231
-
libev=4.33
-
libffi=3.4.2
-
libgfortran=5.0.0
-
libgfortran5=9.3.0
-
libgirepository=1.70.0
-
libglib=2.70.1
-
libiconv=1.16
-
liblapack=3.9.0
-
libllvm13=13.0.1
-
libnghttp2=1.46.0
-
libopenblas=0.3.18
-
libpng=1.6.37
-
librsvg=2.50.3
-
libsodium=1.0.18
-
libssh2=1.10.0
-
libtiff=4.3.0
-
libwebp-base=1.2.1
-
libxcb=1.13
-
libxml2=2.9.10
-
libzlib=1.2.11
-
llvm-openmp=12.0.1
-
lz4-c=1.9.3
-
markupsafe=2.0.1
-
matplotlib=3.5.0
-
matplotlib-base=3.5.0
-
matplotlib-inline=0.1.3
-
mistune=0.8.4
-
munkres=1.0.7
-
mysql-common=8.0.28
-
nbclient=0.5.9
-
nbconvert=6.3.0
-
nbformat=5.1.3
-
ncurses=6.2
-
nest-asyncio=1.5.1
-
notebook=6.4.6
-
nspr=4.32
-
numexpr=2.8.0
-
olefile=0.46
-
openjpeg=2.4.0
-
openssl=3.0.0
-
packaging=21.3
-
pandoc=2.16.1
-
pandocfilters=1.5.0
-
pango=1.42.4
-
parso=0.8.2
-
pcre=8.45
-
pdbpp=0.10.3
-
pexpect=4.8.0
-
pickleshare=0.7.5
-
pillow=8.4.0
-
pip=21.3.1
-
pixman=0.38.0
-
prometheus_client=0.12.0
-
prompt-toolkit=3.0.22
-
prompt_toolkit=3.0.22
-
pthread-stubs=0.4
-
ptyprocess=0.7.0
-
pycairo=1.20.1
-
pycparser=2.21
-
pygments=2.10.0
-
pygobject=3.42.0
-
pyopenssl=22.0.0
-
pyparsing=3.0.6
-
pyqt=5.9.2
-
pyqt5-sip=4.19.18
-
pyrepl=0.9.0
-
pyrsistent=0.18.0
-
pysocks=1.7.1
-
python=3.7.12
-
python-dateutil=2.8.2
-
python_abi=3.7
-
pytz=2021.3
-
pyzmq=22.3.0
-
qt=5.9.7
-
qtconsole=5.2.0
-
qtconsole-base=5.2.2
-
qtpy=1.11.2
-
readline=8.1
-
requests=2.27.1
-
send2trash=1.8.0
-
setuptools=59.2.0
-
sigcpp-2.0=2.10.7
-
sip=4.19.8
-
six=1.16.0
-
sparsehash=2.0.4
-
sqlite=3.36.0
-
terminado=0.12.1
-
testpath=0.5.0
-
tk=8.6.11
-
tornado=6.1
-
traitlets=5.1.1
-
typing_extensions=4.0.0
-
unicodedata2=13.0.0.post2
-
urllib3=1.26.8
-
wcwidth=0.2.5
-
webencodings=0.5.1
-
wheel=0.37.0
-
widgetsnbextension=3.5.2
-
wmctrl=0.4
-
xorg-libxau=1.0.9
-
xorg-libxdmcp=1.1.3
-
xz=5.2.5
-
zeromq=4.3.4
-
zipp=3.6.0
-
zlib=1.2.11
-
zstandard=0.16.0
-
zstd=1.5.0
-
pip
:
-
appdirs==1.4.4
-
beautifulsoup4==4.10.0
-
biodigest==0.2.4
-
bioservices==1.10.1
-
biothings-client==0.2.6
-
bs4==0.0.1
-
cattrs==22.1.0
-
colorama==0.4.5
-
colorlog==6.7.0
-
cssselect==1.1.0
-
domino-python==0.1.1
-
easydev==0.12.0
-
exceptiongroup==1.0.0rc9
-
fake-useragent==0.1.11
-
gevent==21.12.0
-
graph-tools==1.5
-
greenlet==1.1.3
-
grequests==0.6.0
-
gseapy==0.10.5
-
joblib==1.2.0
-
lxml==4.7.1
-
networkx==2.4
-
numpy==1.18.1
-
pandas==1.0.1
-
parse==1.19.0
-
patsy==0.5.2
-
pcst-fast==1.0.7
-
perlcompat==1.1
-
psutil==5.9.0
-
pybind11==2.8.1
-
pyee==8.2.2
-
pyppeteer==1.0.2
-
pyquery==1.4.3
-
pytess==1.0.0
-
python-louvain==0.14
-
requests-cache==0.9.6
-
requests-html==0.10.0
-
scipy==1.4.1
-
seaborn==0.11.2
-
soupsieve==2.3.1
-
statsmodels==0.11.0
-
suds-community==1.1.2
-
tqdm==4.62.3
-
url-normalize==1.4.3
-
w3lib==1.22.0
-
websockets==10.1
-
wrapt==1.14.1
-
xmltodict==0.13.0
-
zope-event==4.5.0
-
zope-interface==5.4.0
prefix
:
/Users/Mia/opt/anaconda3/envs/cami
-
python=3.7
-
graph-tool=2.45
-
networkx
-
pandas
-
numpy
-
jupyter
-
pip
-
matplotlib
-
statsmodels
prefix
:
/Users/Mia/opt/anaconda3/envs/cami_env
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