alethomas
commented
3 years ago Environment:
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- trinity =2.12.0Open alethomas opened 3 years ago
alethomas
commented
3 years ago Environment:
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- trinity =2.12.0# packages in environment at /home/alex/repo/snakemake-workflow-sars-cov2/.snakemake/conda/34fa30aeed90bbcef1c9c71d66ed877d:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
binutils_impl_linux-64 2.35.1 h193b22a_2 conda-forge
binutils_linux-64 2.35 h67ddf6f_30 conda-forge
bioconductor-annotate 1.68.0 r40_0 bioconda
bioconductor-annotationdbi 1.52.0 r40_0 bioconda
bioconductor-biobase 2.50.0 r40h037d062_0 bioconda
bioconductor-biocfilecache 1.14.0 r40_0 bioconda
bioconductor-biocgenerics 0.36.0 r40_0 bioconda
bioconductor-biocparallel 1.24.0 r40h5f743cb_0 bioconda
bioconductor-biomart 2.46.0 r40_0 bioconda
bioconductor-biostrings 2.58.0 r40h037d062_0 bioconda
bioconductor-ctc 1.64.0 r40_0 bioconda
bioconductor-delayedarray 0.16.0 r40h037d062_0 bioconda
bioconductor-deseq2 1.30.0 r40h5f743cb_0 bioconda
bioconductor-dexseq 1.36.0 r40_0 bioconda
bioconductor-edger 3.32.0 r40h5f743cb_0 bioconda
bioconductor-genefilter 1.72.0 r40hc6cf775_0 bioconda
bioconductor-genelendatabase 1.26.0 r40_0 bioconda
bioconductor-geneplotter 1.68.0 r40_0 bioconda
bioconductor-genomeinfodb 1.26.0 r40_0 bioconda
bioconductor-genomeinfodbdata 1.2.4 r40_0 bioconda
bioconductor-genomicalignments 1.26.0 r40h037d062_0 bioconda
bioconductor-genomicfeatures 1.42.0 r40_0 bioconda
bioconductor-genomicranges 1.42.0 r40h037d062_0 bioconda
bioconductor-go.db 3.12.1 r40_0 bioconda
bioconductor-goseq 1.42.0 r40_0 bioconda
bioconductor-iranges 2.24.0 r40h037d062_0 bioconda
bioconductor-limma 3.46.0 r40h037d062_0 bioconda
bioconductor-matrixgenerics 1.2.0 r40_0 bioconda
bioconductor-qvalue 2.22.0 r40_0 bioconda
bioconductor-rhtslib 1.22.0 r40h037d062_0 bioconda
bioconductor-rsamtools 2.6.0 r40h5f743cb_0 bioconda
bioconductor-rtracklayer 1.50.0 r40h9bb0e53_1 bioconda
bioconductor-s4vectors 0.28.0 r40h037d062_0 bioconda
bioconductor-summarizedexperiment 1.20.0 r40_0 bioconda
bioconductor-xvector 0.30.0 r40h037d062_0 bioconda
bioconductor-zlibbioc 1.36.0 r40h037d062_0 bioconda
bowtie 1.3.0 py38hed8969a_1 bioconda
bowtie2 2.4.2 py38h1c8e9b9_1 bioconda
bwidget 1.9.14 0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h7f98852_1 conda-forge
ca-certificates 2021.1.19 h06a4308_1
cairo 1.16.0 hcf35c78_1003 conda-forge
certifi 2020.12.5 py38h578d9bd_1 conda-forge
curl 7.75.0 h979ede3_0 conda-forge
fontconfig 2.13.1 hba837de_1004 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h516909a_0 conda-forge
gcc_impl_linux-64 7.5.0 habd7529_18 conda-forge
gcc_linux-64 7.5.0 h47867f9_30 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
gfortran_impl_linux-64 7.5.0 h56cb351_18 conda-forge
gfortran_linux-64 7.5.0 h78c8a43_30 conda-forge
glib 2.68.0 h9c3ff4c_1 conda-forge
glib-tools 2.68.0 h9c3ff4c_1 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
graphite2 1.3.14 h23475e2_0
gsl 2.6 he838d99_2 conda-forge
gxx_impl_linux-64 7.5.0 hd0bb8aa_18 conda-forge
gxx_linux-64 7.5.0 h555fc39_30 conda-forge
harfbuzz 2.4.0 h9f30f68_3 conda-forge
htslib 1.10.2 hd3b49d5_1 bioconda
icu 64.2 he1b5a44_1 conda-forge
jemalloc 5.2.1 h9c3ff4c_5 conda-forge
jpeg 9d h516909a_0 conda-forge
kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge
kmer-jellyfish 2.3.0 hc9558a2_1 bioconda
krb5 1.17.2 h926e7f8_0 conda-forge
ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge
libblas 3.8.0 17_openblas conda-forge
libcblas 3.8.0 17_openblas conda-forge
libcurl 7.75.0 hc4aaa36_0 conda-forge
libdeflate 1.6 h516909a_0 conda-forge
libedit 3.1.20210216 h27cfd23_1
libev 4.33 h516909a_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-devel_linux-64 7.5.0 hda03d7c_18 conda-forge
libgcc-ng 9.3.0 h2828fa1_18 conda-forge
libgfortran-ng 7.5.0 h14aa051_18 conda-forge
libgfortran4 7.5.0 h14aa051_18 conda-forge
libglib 2.68.0 h3e27bee_1 conda-forge
libgomp 9.3.0 h2828fa1_18 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.8.0 17_openblas conda-forge
libnghttp2 1.43.0 h812cca2_0 conda-forge
libopenblas 0.3.10 pthreads_hb3c22a3_5 conda-forge
libpng 1.6.37 hed695b0_2 conda-forge
libssh2 1.9.0 ha56f1ee_6 conda-forge
libstdcxx-devel_linux-64 7.5.0 hb016644_18 conda-forge
libstdcxx-ng 9.3.0 h6de172a_18 conda-forge
libtiff 4.2.0 hdc55705_0 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp-base 1.2.0 h7f98852_2 conda-forge
libxcb 1.14 h7b6447c_0
libxml2 2.9.10 hee79883_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_0 conda-forge
make 4.3 hd18ef5c_1 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
numpy 1.20.1 py38h18fd61f_0 conda-forge
openjdk 11.0.1 h516909a_1016 conda-forge
openssl 1.1.1j h7f98852_0 conda-forge
pandoc 2.12 h7f98852_0 conda-forge
pango 1.42.4 h7062337_4 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pcre2 10.35 h032f7d1_2 conda-forge
perl 5.32.0 h36c2ea0_0 conda-forge
pip 21.0.1 pyhd8ed1ab_0 conda-forge
pixman 0.38.0 h516909a_1003 conda-forge
python 3.8.8 hffdb5ce_0_cpython conda-forge
python_abi 3.8 1_cp38 conda-forge
r-amap 0.8_18 r40h43222d4_2 conda-forge
r-ape 5.4_1 r40h51c796c_0 conda-forge
r-argparse 2.0.3 r40hc72bb7e_1 conda-forge
r-askpass 1.1 r40hcdcec82_2 conda-forge
r-assertthat 0.2.1 r40h6115d3f_2 conda-forge
r-backports 1.2.1 r40hcfec24a_0 conda-forge
r-base 4.0.2 h95c6c4b_0 conda-forge
r-base64enc 0.1_3 r40hcdcec82_1004 conda-forge
r-bh 1.75.0_0 r40hc72bb7e_0 conda-forge
r-biasedurn 1.07 r40h0357c0b_1004 conda-forge
r-bit 4.0.4 r40hcdcec82_0 conda-forge
r-bit64 4.0.5 r40hcdcec82_0 conda-forge
r-bitops 1.0_6 r40hcdcec82_1004 conda-forge
r-blob 1.2.1 r40h6115d3f_1 conda-forge
r-brio 1.1.1 r40hcfec24a_0 conda-forge
r-broom 0.7.5 r40hc72bb7e_0 conda-forge
r-cachem 1.0.4 r40hcfec24a_0 conda-forge
r-callr 3.5.1 r40h142f84f_0 conda-forge
r-catools 1.18.1 r40h03ef668_0 conda-forge
r-cellranger 1.1.0 r40h6115d3f_1003 conda-forge
r-cli 2.3.1 r40hc72bb7e_0 conda-forge
r-clipr 0.7.1 r40h142f84f_0 conda-forge
r-cluster 2.1.0 r40h31ca83e_4 conda-forge
r-colorspace 2.0_0 r40h9e2df91_0 conda-forge
r-cpp11 0.2.6 r40hc72bb7e_0 conda-forge
r-crayon 1.4.1 r40hc72bb7e_0 conda-forge
r-curl 4.3 r40hcdcec82_1 conda-forge
r-dbi 1.1.1 r40hc72bb7e_0 conda-forge
r-dbplyr 2.1.0 r40hc72bb7e_0 conda-forge
r-desc 1.3.0 r40hc72bb7e_0 conda-forge
r-diffobj 0.3.3 r40hcfec24a_0 conda-forge
r-digest 0.6.27 r40h1b71b39_0 conda-forge
r-dplyr 1.0.5 r40h03ef668_0 conda-forge
r-ellipsis 0.3.1 r40hcdcec82_0 conda-forge
r-evaluate 0.14 r40h6115d3f_2 conda-forge
r-fansi 0.4.2 r40hcfec24a_0 conda-forge
r-farver 2.1.0 r40h03ef668_0 conda-forge
r-fastcluster 1.1.25 r40hc99cbb1_1004 conda-forge
r-fastmap 1.1.0 r40h03ef668_0 conda-forge
r-fastmatch 1.1_0 r40hcdcec82_1005 conda-forge
r-findpython 1.0.7 r40hc72bb7e_0 conda-forge
r-forcats 0.5.1 r40hc72bb7e_0 conda-forge
r-formatr 1.8 r40hc72bb7e_0 conda-forge
r-fs 1.5.0 r40h0357c0b_0 conda-forge
r-futile.logger 1.4.3 r40h6115d3f_1003 conda-forge
r-futile.options 1.0.1 r40h6115d3f_1002 conda-forge
r-generics 0.1.0 r40hc72bb7e_0 conda-forge
r-getopt 1.20.3 r40_2 conda-forge
r-ggplot2 3.3.3 r40hc72bb7e_0 conda-forge
r-glue 1.4.2 r40hcfec24a_0 conda-forge
r-gplots 3.1.1 r40hc72bb7e_0 conda-forge
r-gtable 0.3.0 r40h6115d3f_3 conda-forge
r-gtools 3.8.2 r40hcdcec82_1 conda-forge
r-haven 2.3.1 r40hde08347_0 conda-forge
r-highr 0.8 r40h6115d3f_2 conda-forge
r-hms 1.0.0 r40hc72bb7e_0 conda-forge
r-htmltools 0.5.1.1 r40h03ef668_0 conda-forge
r-httr 1.4.2 r40h6115d3f_0 conda-forge
r-hwriter 1.3.2 r40h6115d3f_1003 conda-forge
r-igraph 1.2.6 r40h084b37e_1 conda-forge
r-isoband 0.2.4 r40h03ef668_0 conda-forge
r-jsonlite 1.7.2 r40hcfec24a_0 conda-forge
r-kernsmooth 2.23_18 r40h7679c2e_0 conda-forge
r-knitr 1.31 r40hc72bb7e_0 conda-forge
r-labeling 0.4.2 r40h142f84f_0 conda-forge
r-lambda.r 1.2.4 r40h6115d3f_1 conda-forge
r-lattice 0.20_41 r40hcfec24a_3 conda-forge
r-lifecycle 1.0.0 r40hc72bb7e_0 conda-forge
r-locfit 1.5_9.4 r40hcdcec82_1 conda-forge
r-lubridate 1.7.10 r40h03ef668_0 conda-forge
r-magrittr 2.0.1 r40hcfec24a_1 conda-forge
r-markdown 1.1 r40hcfec24a_1 conda-forge
r-mass 7.3_53.1 r40hcfec24a_0 conda-forge
r-matrix 1.3_2 r40he454529_0 conda-forge
r-matrixstats 0.58.0 r40hcfec24a_0 conda-forge
r-memoise 2.0.0 r40hc72bb7e_0 conda-forge
r-mgcv 1.8_34 r40he454529_0 conda-forge
r-mime 0.10 r40hcfec24a_0 conda-forge
r-modelr 0.1.8 r40h6115d3f_0 conda-forge
r-munsell 0.5.0 r40h6115d3f_1003 conda-forge
r-nlme 3.1_150 r40h31ca83e_0 conda-forge
r-openssl 1.4.3 r40he5c4762_0 conda-forge
r-phangorn 2.6.2 r40h03ef668_0 conda-forge
r-pillar 1.5.1 r40hc72bb7e_0 conda-forge
r-pkgbuild 1.2.0 r40hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r40h6115d3f_1 conda-forge
r-pkgload 1.2.0 r40h03ef668_0 conda-forge
r-plogr 0.2.0 r40h6115d3f_1003 conda-forge
r-plyr 1.8.6 r40h0357c0b_1 conda-forge
r-praise 1.0.0 r40h6115d3f_1004 conda-forge
r-prettyunits 1.1.1 r40h6115d3f_1 conda-forge
r-processx 3.4.5 r40hcfec24a_0 conda-forge
r-progress 1.2.2 r40h6115d3f_2 conda-forge
r-ps 1.6.0 r40hcfec24a_0 conda-forge
r-purrr 0.3.4 r40hcdcec82_1 conda-forge
r-quadprog 1.5_8 r40hed91ed1_3 conda-forge
r-r6 2.5.0 r40hc72bb7e_0 conda-forge
r-rappdirs 0.3.3 r40hcfec24a_0 conda-forge
r-rcolorbrewer 1.1_2 r40h6115d3f_1003 conda-forge
r-rcpp 1.0.6 r40h03ef668_0 conda-forge
r-rcpparmadillo 0.10.2.2.0 r40h306847c_0 conda-forge
r-rcurl 1.98_1.3 r40hcfec24a_0 conda-forge
r-readr 1.4.0 r40h1b71b39_0 conda-forge
r-readxl 1.3.1 r40hde08347_4 conda-forge
r-rematch 1.0.1 r40h6115d3f_1003 conda-forge
r-rematch2 2.1.2 r40h6115d3f_1 conda-forge
r-reprex 1.0.0 r40hc72bb7e_0 conda-forge
r-reshape2 1.4.4 r40h0357c0b_1 conda-forge
r-rlang 0.4.10 r40hcfec24a_0 conda-forge
r-rmarkdown 2.7 r40hc72bb7e_0 conda-forge
r-rprojroot 2.0.2 r40hc72bb7e_0 conda-forge
r-rsqlite 2.2.4 r40h03ef668_0 conda-forge
r-rstudioapi 0.13 r40hc72bb7e_0 conda-forge
r-rvest 1.0.0 r40hc72bb7e_0 conda-forge
r-scales 1.1.1 r40h6115d3f_0 conda-forge
r-selectr 0.4_2 r40h6115d3f_1 conda-forge
r-sm 2.2_5.6 r40h31ca83e_1004 conda-forge
r-snow 0.4_3 r40h6115d3f_1002 conda-forge
r-statmod 1.4.35 r40h6e990d7_1 conda-forge
r-stringi 1.4.6 r40h0e574ca_2 conda-forge
r-stringr 1.4.0 r40h6115d3f_2 conda-forge
r-survival 3.2_10 r40hcfec24a_0 conda-forge
r-sys 3.4 r40hcdcec82_0 conda-forge
r-testthat 3.0.2 r40h03ef668_0 conda-forge
r-tibble 3.1.0 r40hcfec24a_1 conda-forge
r-tidyr 1.1.3 r40h03ef668_0 conda-forge
r-tidyselect 1.1.0 r40h6115d3f_0 conda-forge
r-tidyverse 1.3.0 r40h6115d3f_2 conda-forge
r-tinytex 0.30 r40hc72bb7e_0 conda-forge
r-utf8 1.2.1 r40hcfec24a_0 conda-forge
r-vctrs 0.3.6 r40hcfec24a_0 conda-forge
r-vioplot 0.3.5 r40h6115d3f_0 conda-forge
r-viridislite 0.3.0 r40h6115d3f_1003 conda-forge
r-waldo 0.2.5 r40hc72bb7e_0 conda-forge
r-withr 2.4.1 r40hc72bb7e_0 conda-forge
r-xfun 0.20 r40hcfec24a_0 conda-forge
r-xml 3.99_0.6 r40hcfec24a_0 conda-forge
r-xml2 1.3.2 r40h0357c0b_1 conda-forge
r-xtable 1.8_4 r40h6115d3f_3 conda-forge
r-yaml 2.2.1 r40hcfec24a_1 conda-forge
r-zeallot 0.1.0 r40h6115d3f_1002 conda-forge
r-zoo 1.8_9 r40hcfec24a_0 conda-forge
readline 8.1 h27cfd23_0
salmon 1.4.0 hf69c8f4_0 bioconda
samtools 1.10 h2e538c0_3 bioconda
sed 4.8 he412f7d_0 conda-forge
setuptools 52.0.0 py38h06a4308_0
sqlite 3.35.2 h74cdb3f_0 conda-forge
sysroot_linux-64 2.12 h77966d4_13 conda-forge
tbb 2021.1.1 h4bd325d_1 conda-forge
tk 8.6.10 hed695b0_1 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
trimmomatic 0.39 1 bioconda
trinity 2.12.0 h5ef6573_0 bioconda
wheel 0.36.2 pyhd3deb0d_0 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.0 h36c2ea0_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.4.9 ha95c52a_0 conda-forge
mbargull
commented
3 years ago The problem here is TBB. The TBB version 2021.1.1 broke backward compatibility and older builds with <=2020.2 did not pin (via run_exports) that version, unfortunately.
We are in the process of kicking off a mass rebuild of our packages with which updated 2020.2 builds will get properly pinned TBB versions.
A temporary workaround is to explicitly install tbb <2021 alongside the requested to ensure a compatible version gets installed.
mfansler
commented
3 years ago Just ran across this issue myself. Specifically, I was recreating a previous pipeline that had pinned salmon=1.3.0 and since there was no constraint on tbb it pulled the 2021 version. This was leading to a missing symbol issue. I can confirm that adding tbb=2020.2 resolved the issue.
Trinity in version 2.12.0 (down to 2.9) doesn't seem to be able to install all its dependencies properly. When running with Snakemake, the depending salmon cannot be found.