fbaumdicker / spacerplacer Goto Github PK
View Code? Open in Web Editor NEWancestral reconstruction and likelihood analysis for CRISPR spacer arrays
License: GNU General Public License v3.0
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install
Thanks for this tool! I did not find the right way to install the software. Could you please advise me?
Minimal conda environment file
Hi,
thank you for this software!
I noticed the environment.yml file provided is unfortunately difficult to use, as it was probably created using the conda env export --name my_env > myenv.yml command.
This creates a very long file with all packages listed with and pinned with their current versions. Unfortunately, this is very platform and python kernel version dependent. In my case, this led to many "environment cannot be solved" issues.
The conda documentation suggests using the option conda env export --from-history > environment.yml, which only lists all the packages that were installed from the CLI (e.g. conda install pandas==1.3.4), making the resulting file very minimal and cross-platform and cross-kernel-version compatible (please note that this excludes all pip installations!.
Using the provided requirements.txt, I manually created the following "minimal" environment file, which should work on most systems and kernel versions, and should include all of the necessary packages. Please feel free to use it or add any requirements that I may have overlooked.
name: spacerplacer_minimal
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- numpy>=1.21.4
- pandas>=1.3.4
- seaborn>=0.11.2
- matplotlib>=3.4.3
- scipy>=1.7.1
- ete3>=3.1.2
- palettable>=3.3.0
- pyqt>=5.15.6
- graphviz>=0.20.1
- sympy>=1.11.1
- dill>=0.3.5.1
- mafft>=7.490
- biopython>=1.79
- python-graphviz>=0.17
On my system (Ubuntu 22.04 LTS), this produced the following environment at the time of writing:
# packages in environment:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.11 hd590300_1 conda-forge
atk-1.0 2.38.0 hd4edc92_1 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
biopython 1.83 py312h98912ed_0 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
contourpy 1.2.0 py312h8572e83_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
dill 0.3.8 pyhd8ed1ab_0 conda-forge
ete3 3.1.3 pyhd8ed1ab_0 conda-forge
expat 2.6.1 h59595ed_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.49.0 py312h98912ed_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gawk 5.3.0 ha916aea_0 conda-forge
gdk-pixbuf 2.42.10 h829c605_5 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
glib 2.80.0 hf2295e7_0 conda-forge
glib-tools 2.80.0 hde27a5a_0 conda-forge
gmp 6.3.0 h59595ed_1 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
graphviz 9.0.0 h78e8752_1 conda-forge
gst-plugins-base 1.22.9 h8e1006c_0 conda-forge
gstreamer 1.22.9 h98fc4e7_0 conda-forge
gtk2 2.24.33 h280cfa0_4 conda-forge
gts 0.7.6 h977cf35_4 conda-forge
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py312h8572e83_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 21_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 21_linux64_openblas conda-forge
libclang 15.0.7 default_hb11cfb5_4 conda-forge
libclang13 15.0.7 default_ha2b6cf4_4 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.1 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libgfortran-ng 13.2.0 h69a702a_5 conda-forge
libgfortran5 13.2.0 ha4646dd_5 conda-forge
libglib 2.80.0 hf2295e7_0 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libgpg-error 1.48 h71f35ed_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 21_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 16.2 h33b98f1_0 conda-forge
librsvg 2.56.3 he3f83f7_1 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsqlite 3.45.1 h2797004_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libsystemd0 255 h3516f8a_1 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.3.2 h658648e_1 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.6.0 hd429924_1 conda-forge
libxml2 2.12.5 h232c23b_0 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lxml 5.1.0 py312h37b5203_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
mafft 7.520 h031d066_3 bioconda
matplotlib 3.8.3 py312h7900ff3_0 conda-forge
matplotlib-base 3.8.3 py312he5832f3_0 conda-forge
mpfr 4.2.1 h9458935_0 conda-forge
mpg123 1.32.4 h59595ed_0 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.33 hf1915f5_6 conda-forge
mysql-libs 8.0.33 hca2cd23_6 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.98 h1d7d5a4_0 conda-forge
numpy 1.26.4 py312heda63a1_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.2.1 hd590300_0 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
palettable 3.3.3 pyhd8ed1ab_0 conda-forge
pandas 2.2.1 py312hfb8ada1_0 conda-forge
pango 1.52.1 ha41ecd1_0 conda-forge
patsy 0.5.6 pyhd8ed1ab_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
pillow 10.2.0 py312hf3581a9_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
ply 3.11 py_1 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pulseaudio-client 16.1 hb77b528_5 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py312h949fe66_5 conda-forge
pyqt5-sip 12.12.2 py312h30efb56_5 conda-forge
python 3.12.2 hab00c5b_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-graphviz 0.20.1 pyh22cad53_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.12 4_cp312 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
qt-main 5.15.8 h5810be5_19 conda-forge
readline 8.2 h8228510_1 conda-forge
scipy 1.12.0 py312heda63a1_2 conda-forge
seaborn 0.13.2 hd8ed1ab_0 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_0 conda-forge
setuptools 69.1.1 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py312h30efb56_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
statsmodels 0.14.1 py312hc7c0aa3_0 conda-forge
sympy 1.12 pyh04b8f61_3 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py312h98912ed_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.41 hd590300_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Best wishes,
Richard
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