Error installing seqret formula (M3 mac)

[AceM1188]

Hi there,

I'm setting up a brand new bioinformatic computer for my lab with this (thank you btw). However, I'm running into an error specifically with installing the seqret formula. All other formula have installed without issue following the instructions provided.

Machine specs: Apple M3 Pro, OS: Sonoma 14.5. Xcode and OS are both up to date.
Of note, anaconda has not been separately installed.

I have tried both installing by the "Quick Installation" method as well as the "Step-by-Step" method. (I uninstalled everything using the code in the "Redo Installation" instructions prior to repeating using the Step-by-Step method). After both efforts, I receive the following error when trying to individually install seqret:

$ micromamba install seqret
bioconda/osx-64 No change
bioconda/noarch @ 2.3MB/s 2.3s
conda-forge/noarch 15.8MB @ 3.5MB/s 4.5s
conda-forge/osx-64 32.2MB @ 5.2MB/s 6.2s

Pinned packages:
- python 3.10.*

error libmamba Could not solve for environment specs
The following package could not be installed
└─ seqret does not exist (perhaps a typo or a missing channel).
critical libmamba Could not solve for environment specs

Of note, below are my channel priorities:
$ micromamba config list
channels:
- conda-forge
- bioconda
channel_priority: strict

Any advice on how best to proceed to ensure a complete installation? Of course, please do not hesitate to let me know of any other info you need on my end.

Thanks in advance.

[ialbert]

seqret is part of the emboss package, so the installation would be

micromamba install emboss

[AceM1188]

Also did this which did not generate any errors. Here's the output of micromamba list

$ micromamba list
List of packages in environment: "/Users/mherna17/micromamba/envs/bioinfo"

Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────
agate 1.12.0 pyh707e725_0 conda-forge
agate-dbf 0.2.3 pyhd8ed1ab_0 conda-forge
agate-excel 0.2.3 py_0 conda-forge
agate-sql 0.7.2 pyhd8ed1ab_0 conda-forge
aria2 1.37.0 h21e4757_2 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
bcftools 1.20 h0126a07_1 bioconda
bedtools 2.31.1 hdd9cfa2_2 bioconda
bioawk 1.0 h10309d6_12 bioconda
biopython 1.84 py310h936d840_0 conda-forge
blast 2.6.0 boost1.64_2 bioconda
bowtie2 2.5.4 h8fd0fe2_2 bioconda
bwa 0.7.18 h10309d6_1 bioconda
bzip2 1.0.8 hfdf4475_7 conda-forge
c-ares 1.32.3 h51dda26_0 conda-forge
ca-certificates 2024.7.4 h8857fd0_0 conda-forge
cffi 1.16.0 py310hdca579f_0 conda-forge
cld2-cffi 0.1.4 py310had63691_1005 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
csvkit 2.0.1 pyhd8ed1ab_0 conda-forge
csvtk 0.30.0 h527b516_2 bioconda
datamash 1.8 h37ebe6b_0 conda-forge
dbfread 2.0.7 py_0 conda-forge
emboss 6.5.7 2 bioconda
et_xmlfile 1.1.0 pyhd8ed1ab_0 conda-forge
expat 2.6.2 h73e2aa4_0 conda-forge
fastp 0.23.4 h1d47e6f_5 bioconda
fastqc 0.12.1 hdfd78af_0 bioconda
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
fontconfig 2.14.2 h5bb23bf_0 conda-forge
freebayes 1.3.6 hd0edb90_5 bioconda
freetype 2.12.1 h60636b9_2 conda-forge
future 1.0.0 pyhd8ed1ab_0 conda-forge
gawk 5.3.0 h2c496e9_0 conda-forge
gettext 0.22.5 h5ff76d1_2 conda-forge
gettext-tools 0.22.5 h5ff76d1_2 conda-forge
gmp 6.3.0 hf036a51_2 conda-forge
greenlet 3.0.3 py310h5daac23_0 conda-forge
gsl 2.7 h93259b0_0 conda-forge
hisat2 2.2.1 h7133b54_6 bioconda
htslib 1.20 hec81eee_2 bioconda
icu 75.1 h120a0e1_0 conda-forge
isa-l 2.31.0 hfdf4475_2 conda-forge
isodate 0.6.1 pyhd8ed1ab_0 conda-forge
jq 1.7.1 h10d778d_0 conda-forge
krb5 1.21.3 h37d8d59_0 conda-forge
leather 0.3.4 pyhd8ed1ab_0 conda-forge
libasprintf 0.22.5 h5ff76d1_2 conda-forge
libasprintf-devel 0.22.5 h5ff76d1_2 conda-forge
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libcurl 8.9.1 hfcf2730_0 conda-forge
libcxx 18.1.8 hef8daea_2 conda-forge
libdeflate 1.20 h49d49c5_0 conda-forge
libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 h10d778d_2 conda-forge
libexpat 2.6.2 h73e2aa4_0 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libgcc 4.8.5 hdbeacc1_10 conda-forge
libgettextpo 0.22.5 h5ff76d1_2 conda-forge
libgettextpo-devel 0.22.5 h5ff76d1_2 conda-forge
libgfortran 3.0.1 0 conda-forge
libhwloc 2.11.1 default_h456cccd_1000 conda-forge
libiconv 1.17 hd75f5a5_2 conda-forge
libidn2 2.3.7 h10d778d_0 conda-forge
libintl 0.22.5 h5ff76d1_2 conda-forge
libintl-devel 0.22.5 h5ff76d1_2 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libnghttp2 1.58.0 h64cf6d3_1 conda-forge
libopenblas 0.3.7 hd44dcd8_1 conda-forge
libpng 1.6.43 h92b6c6a_0 conda-forge
libsqlite 3.46.0 h1b8f9f3_0 conda-forge
libssh2 1.11.0 hd019ec5_0 conda-forge
libunistring 0.9.10 h0d85af4_0 conda-forge
libxml2 2.12.7 heaf3512_4 conda-forge
libzlib 1.3.1 h87427d6_1 conda-forge
llvm-openmp 18.1.8 h15ab845_0 conda-forge
loguru 0.7.2 py310h2ec42d9_1 conda-forge
mafft 7.526 hfdf4475_0 conda-forge
make 4.3 h22f3db7_1 conda-forge
minimap2 2.1.1 0 bioconda
mpfr 4.2.1 hc80595b_2 conda-forge
ncbi-datasets-cli 16.25.0 h694c41f_0 conda-forge
ncurses 6.5 h5846eda_0 conda-forge
numpy 1.22.4 py310hed37afb_0 conda-forge
oniguruma 6.9.9 h10d778d_0 conda-forge
openjdk 22.0.1 h1c1aa8c_1 conda-forge
openpyxl 3.1.2 py310h6729b98_1 conda-forge
openssl 3.3.1 h87427d6_2 conda-forge
pandas 2.2.2 py310hbf2a7f0_1 conda-forge
parallel 20240722 h694c41f_0 conda-forge
parsedatetime 2.4 py_1 conda-forge
perl 5.32.1 7_h10d778d_perl5 conda-forge
perl-test-harness 3.44 pl5321hd8ed1ab_0 conda-forge
perl-text-csv 2.02 pl5321hd8ed1ab_0 conda-forge
pip 24.2 pyhd8ed1ab_0 conda-forge
polypolish 0.6.0 h48ddd8c_1 bioconda
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pyicu 2.13.1 py310h3ba615c_1 conda-forge
pypolca 0.3.1 pyhdfd78af_0 bioconda
python 3.10.14 h00d2728_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-slugify 8.0.4 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
pytimeparse 1.1.8 py_0 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py310h6729b98_1 conda-forge
readline 8.2 h9e318b2_1 conda-forge
samtools 1.20 h94387ee_1 bioconda
seqkit 2.8.2 h527b516_1 bioconda
seqtk 1.2 0 bioconda
setuptools 71.0.4 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snpeff 5.0 hdfd78af_1 bioconda
sqlalchemy 1.4.49 py310hb372a2b_1 conda-forge
subread 1.5.3 0 bioconda
tabixpp 1.1.2 he6e7409_3 bioconda
tbb 2021.12.0 h3c5361c_3 conda-forge
text-unidecode 1.3 pyhd8ed1ab_1 conda-forge
tk 8.6.13 h1abcd95_1 conda-forge
trimmomatic 0.39 hdfd78af_2 bioconda
tzdata 2024a h0c530f3_0 conda-forge
ucsc-bedgraphtobigwig 357 1 bioconda
vcflib 1.0.3 h0546b6b_4 bioconda
wget 1.21.4 hca547e6_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xlrd 2.0.1 pyhd8ed1ab_3 conda-forge
xz 5.2.6 h775f41a_0 conda-forge
yaml 0.2.5 h0d85af4_2 conda-forge
zlib 1.3.1 h87427d6_1 conda-forge
zstd 1.5.6 h915ae27_0 conda-forge

However, when trying to execute the seqret formula I get the following error:
$ seqret
dyld[94411]: Library not loaded: /usr/local/lib/libpq.5.dylib
Referenced from: <879B2B8E-E83F-39A3-A92E-3E70DC2EA07C> /Users/mherna17/micromamba/envs/bioinfo/bin/_seqret
Reason: tried: '/usr/local/lib/libpq.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libpq.5.dylib' (no such file), '/usr/local/lib/libpq.5.dylib' (no such file), '/usr/lib/libpq.5.dylib' (no such file, not in dyld cache)
/Users/mherna17/micromamba/envs/bioinfo/bin/seqret: line 7: 94411 Abort trap: 6 _seqret $@

And when I try embossversion:
$ embossversion
dyld[94425]: Library not loaded: /usr/local/lib/libpq.5.dylib
Referenced from: <AB00148E-B10B-3CE1-A3E0-DA813018CA45> /Users/mherna17/micromamba/envs/bioinfo/bin/_embossversion Reason: tried: '/usr/local/lib/libpq.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libpq.5.dylib' (no such file), '/usr/local/lib/libpq.5.dylib' (no such file), '/usr/lib/libpq.5.dylib' (no such file, not in dyld cache)
/Users/mherna17/micromamba/envs/bioinfo/bin/embossversion: line 7: 94425 Abort trap: 6 _embossversion $@

Any thoughts?

[ialbert]

not sure what that is but try installing into a separate env and run it that way

micromamba create -n emboss emboss

then run via that environment

micromamba run -n emboss seqret

[AceM1188]

Weird indeed.
But installing and running via a separate environment worked!
Thank you!

[ialbert]

seqret has been removed from most content in the book. Most of what seqre could do can be achieved in simpler way with bio fetch etc.

The emboss dependency has now been removed from the installation. If someone needs tools from the Emboss suite they should use the following construct:

# Install emboss into a separate environment.
micromamba create -n emboss emboss


# When an emboss tool is needed, run it in the emboss environment.
micromamba run -n emboss seqret