Mamba install for eukulele=2.0.7 is problematic
g0ddengr opened this issue · 5 comments
Hi,
I have been unable to install a working version of EUKulele/2.0.7 on our HPC. I created and activated a new environment, and then followed the mamba installation instructions here: https://eukulele.readthedocs.io/en/latest/install.html#installing-with-mamba
$ mamba install -c akrinos -c bioconda -c conda-forge EUKulele
This command runs successfully and without error. However, it yields an incomplete installation that lacks dependencies required to perform some EUKulele steps. For starters, I noted that the environment did not include zenodo-get, which was required to download the EukZoo db with the 'EUKulele download --database eukzoo' command. Once I install that with mamba, the database downloads. However, there are more problems. If I run the test data using the 'EUKulele --config curr_config.yaml' command, the pipeline runs but reports no BUSCO results. This is because more dependencies are missing: e.g., BUSCO and TransDecoder (and possibly AUGUSTUS too). BUSCO could not be installed with mamba at this point because of multiple conflicts, namely with biopython.
I removed the environment and started again, this time using a different creation strategy:
$ mamba create -p /eukulele/2.0.7 eukulele busco transdecoder zenodo_get
This approach was able to resolve conflicts and intstall an environment that I assumed included the required dependencies. However, when I run the same test described above 'EUKulele --config curr_config.yaml', the pipeline reports no BUSCO results. The log files indicate that the problem is due to an incompatibility between
the installed busco=4.0.4 and biopython=1.78, which lacks bio.alphabet. I cannot downgrade biopython, and I cannot upgrade busco=4.0.6 without lots of conflicts.
What do I need to change to yield a compatible and working environment?
$ mamba list
packages in environment at /apps/eukulele/2.0.7:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
alsa-lib 1.2.3.2 h166bdaf_0 conda-forge
anyio 3.7.1 pyhd8ed1ab_0 conda-forge
augustus 3.2.2 0 bioconda
bamtools 2.5.2 hdcf5f25_2 bioconda
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_33 conda-forge
bioconductor-seqlogo 1.52.0 r36_0 bioconda
biopython 1.78 py37h5e8e339_2 conda-forge
blast 2.2.31 1 bioconda
boost 1.68.0 py37h8619c78_1001 conda-forge
boost-cpp 1.68.0 h11c811c_1000 conda-forge
brotli-python 1.0.9 py37hd23a5d3_7 conda-forge
busco 4.0.4 pyr36_0 bioconda
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cairo 1.16.0 h18b612c_1001 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py37h43b0acd_1 conda-forge
chardet 5.0.0 py37h89c1867_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
cryptography 38.0.2 py37h38fbfac_1 conda-forge
curl 7.68.0 hf8cf82a_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dendropy 4.5.1 pyh3252c3a_0 bioconda
diamond 0.9.24 ha888412_1 bioconda
dnspython 2.4.2 pyhd8ed1ab_0 conda-forge
eukulele 2.0.7 pyh78b79e7_0 bioconda
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
expat 2.6.1 h59595ed_0 conda-forge
findutils 4.6.0 h166bdaf_1001 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gcc_impl_linux-64 7.5.0 habd7529_20 conda-forge
gcc_linux-64 7.5.0 h47867f9_33 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gfortran_impl_linux-64 7.5.0 h56cb351_20 conda-forge
gfortran_linux-64 7.5.0 h78c8a43_33 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
glib 2.78.4 hfc55251_4 conda-forge
glib-tools 2.78.4 hfc55251_4 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.5 h294904e_1 conda-forge
gxx_impl_linux-64 7.5.0 hd0bb8aa_20 conda-forge
gxx_linux-64 7.5.0 h555fc39_33 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
harfbuzz 2.4.0 h37c48d4_1 conda-forge
hmmer 3.1b2 3 bioconda
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 0.17.3 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_17 conda-forge
kiwisolver 1.4.4 py37h7cecad7_0 conda-forge
krb5 1.16.4 h2fd8d38_0 conda-forge
lcms2 2.14 h6ed2654_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 8_openblas conda-forge
libcblas 3.9.0 8_openblas conda-forge
libcurl 7.68.0 hda55be3_0 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.14 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libexpat 2.6.1 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-devel_linux-64 7.5.0 hda03d7c_20 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgfortran-ng 7.5.0 h14aa051_20 conda-forge
libgfortran4 7.5.0 h14aa051_20 conda-forge
libglib 2.78.4 hf2295e7_4 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libiconv 1.17 hd590300_2 conda-forge
liblapack 3.9.0 8_openblas conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.12 pthreads_hb3c22a3_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libsqlite 3.45.1 h2797004_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 7.5.0 hb016644_20 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libtiff 4.4.0 h82bc61c_5 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.9.9 h13577e0_2 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
make 4.3 hd18ef5c_1 conda-forge
matplotlib-base 3.3.3 py37h0c9df89_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
numpy 1.19.5 py37h3e96413_3 conda-forge
openjdk 11.0.8 hacce0ff_0 conda-forge
openjpeg 2.5.0 h7d73246_1 conda-forge
openssl 1.1.1w hd590300_0 conda-forge
pandas 1.2.0 py37hdc94413_1 conda-forge
pango 1.40.14 he7ab937_1005 conda-forge
pasta 1.7.8 py37h8f50634_4 bioconda
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-app-cpanminus 1.7047 pl5321hd8ed1ab_0 conda-forge
perl-business-isbn 3.007 pl5321hd8ed1ab_0 conda-forge
perl-business-isbn-data 20210112.006 pl5321hd8ed1ab_0 conda-forge
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-db-file 1.855 pl5321h779adbc_1 bioconda
perl-dbi 1.643 pl5321h166bdaf_0 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-test-fatal 0.016 pl5321ha770c72_0 conda-forge
perl-test-warnings 0.031 pl5321ha770c72_0 conda-forge
perl-try-tiny 0.31 pl5321ha770c72_0 conda-forge
perl-uri 5.17 pl5321ha770c72_0 conda-forge
perl-yaml 1.30 pl5321hdfd78af_0 bioconda
pillow 9.2.0 py37h850a105_2 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.38.0 h516909a_1003 conda-forge
prodigal 2.6.3 h031d066_7 bioconda
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pymongo 4.3.2 py37hd23a5d3_0 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 py37h89c1867_5 conda-forge
python 3.7.12 hb7a2778_100_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-wget 3.2 py_0 conda-forge
python_abi 3.7 4_cp37m conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py37h540881e_4 conda-forge
r-assertthat 0.2.1 r36h6115d3f_2 conda-forge
r-backports 1.2.1 r36hcfec24a_0 conda-forge
r-base 3.6.1 h8900bf8_2 conda-forge
r-brio 1.1.2 r36hcfec24a_0 conda-forge
r-callr 3.7.0 r36hc72bb7e_0 conda-forge
r-cli 2.5.0 r36hc72bb7e_0 conda-forge
r-colorspace 2.0_1 r36hcfec24a_0 conda-forge
r-crayon 1.4.1 r36hc72bb7e_0 conda-forge
r-desc 1.3.0 r36hc72bb7e_0 conda-forge
r-diffobj 0.3.4 r36hcfec24a_0 conda-forge
r-digest 0.6.27 r36h03ef668_0 conda-forge
r-ellipsis 0.3.2 r36hcfec24a_0 conda-forge
r-evaluate 0.14 r36h6115d3f_2 conda-forge
r-fansi 0.4.2 r36hcfec24a_0 conda-forge
r-farver 2.1.0 r36h03ef668_0 conda-forge
r-ggplot2 3.3.3 r36hc72bb7e_0 conda-forge
r-glue 1.4.2 r36hcfec24a_0 conda-forge
r-gtable 0.3.0 r36h6115d3f_3 conda-forge
r-isoband 0.2.4 r36h03ef668_0 conda-forge
r-jsonlite 1.7.2 r36hcfec24a_0 conda-forge
r-labeling 0.4.2 r36h142f84f_0 conda-forge
r-lattice 0.20_44 r36hcfec24a_0 conda-forge
r-lifecycle 1.0.0 r36hc72bb7e_0 conda-forge
r-magrittr 2.0.1 r36hcfec24a_1 conda-forge
r-mass 7.3_54 r36hcfec24a_0 conda-forge
r-matrix 1.3_3 r36he454529_0 conda-forge
r-mgcv 1.8_35 r36he454529_0 conda-forge
r-munsell 0.5.0 r36h6115d3f_1003 conda-forge
r-nlme 3.1_150 r36h31ca83e_0 conda-forge
r-pillar 1.6.1 r36hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r36h6115d3f_1 conda-forge
r-pkgload 1.2.1 r36h03ef668_0 conda-forge
r-praise 1.0.0 r36h6115d3f_1004 conda-forge
r-processx 3.5.2 r36hcfec24a_0 conda-forge
r-ps 1.6.0 r36hcfec24a_0 conda-forge
r-r6 2.5.0 r36hc72bb7e_0 conda-forge
r-rcolorbrewer 1.1_2 r36h6115d3f_1003 conda-forge
r-rcpp 1.0.6 r36h03ef668_0 conda-forge
r-rematch2 2.1.2 r36h6115d3f_1 conda-forge
r-rlang 0.4.11 r36hcfec24a_0 conda-forge
r-rprojroot 2.0.2 r36hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r36hc72bb7e_0 conda-forge
r-scales 1.1.1 r36h6115d3f_0 conda-forge
r-testthat 3.0.2 r36h03ef668_0 conda-forge
r-tibble 3.1.2 r36hcfec24a_0 conda-forge
r-utf8 1.2.1 r36hcfec24a_0 conda-forge
r-vctrs 0.3.8 r36hcfec24a_1 conda-forge
r-viridislite 0.4.0 r36hc72bb7e_0 conda-forge
r-waldo 0.2.5 r36hc72bb7e_0 conda-forge
r-withr 2.4.2 r36hc72bb7e_0 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
scipy 1.5.3 py37h8911b10_0 conda-forge
seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
sepp 4.5.1 py37h9ee0642_3 bioconda
setuptools 59.8.0 py37h89c1867_1 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
sqlite 3.45.1 h2c6b66d_0 conda-forge
sysroot_linux-64 2.12 he073ed8_17 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h0c5db8f_5 conda-forge
tornado 6.2 py37h540881e_0 conda-forge
transdecoder 5.7.1 pl5321hdfd78af_0 bioconda
typing-extensions 4.7.1 hd8ed1ab_0 conda-forge
typing_extensions 4.7.1 pyha770c72_0 conda-forge
ujson 5.5.0 py37hd23a5d3_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 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 1.8.4 h0b41bf4_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-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zenodo_get 1.3.4 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Thank you in advance for your help.
Grant
Hi @akrinos ,
This is what I get without the -c akrinos:
$ mamba install -c bioconda -c conda-forge EUKulele
...
Could not solve for environment specs
The following package could not be installed
└─ eukulele is not installable because it requires
└─ biopython 1.78 , which conflicts with any installable versions previously reported.
conda create -n foo --dry-run -c conda-forge -c bioconda EUKulele
This works for me locally. Please make sure to always use conda create. Mamba is not needed anymore if you are using the latest conda version (mamba solver is now integrated into conda). Please also make sure conda-forge has the higher priority over bioconda.
Hi @bgruening @g0ddengr - sorry for missing the reply in March, thank you @bgruening for sharing! @g0ddengr did you ever get the install to work?
@bgruening and @akrinos. Thanks so much! I was able to make the installation without problems.