versions for conda dependencies

[nick-youngblut]

The README states:

conda create -n FLAMES \
    "python>=3.7" samtools pysam minimap2 numpy editdistance \
    -c bioconda -c conda-forge
git clone https://github.com/LuyiTian/FLAMES.git

What are the supported versions for each of the listed conda dependencies?

[maxim-h]

Second that question. The way the environment got resolved for me causes an error in the pipeline

FLAMES error

```sh ### generate transcript count matrix 2024-06-24 15:21:21 Traceback (most recent call last): File "[prefix]/FLAMES/python/sc_long_pipeline.py", line 240, in sc_long_pipeline(args) File "[prefix]//FLAMES/python/sc_long_pipeline.py", line 224, in sc_long_pipeline bc_tr_count_dict, bc_tr_badcov_count_dict, tr_kept = parse_realigned_bam( File "[prefix]//FLAMES/python/count_tr.py", line 126, in parse_r ealigned_bam rec.query_alignment_length)/rec.infer_read_length(), rec.mapping_quality)) AttributeError: 'pysam.calignedsegment.AlignedSegment' object has no attribute 'infer_read_length' ```

Here is how the environment looks looks for me.

Micromamba list ```sh $ micromamba list List of packages in environment: "[HOME]/.micromamba/envs/FLAMES" Name Version Build Channel ──────────────────────────────────────────────────────────────────────────────────────── _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _sysroot_linux-64_curr_repodata_hack 3 h69a702a_14 conda-forge bcftools 1.3.1 h5bf99c6_7 bioconda bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.11.0 h470a237_1 bioconda ca-certificates 2024.6.2 hbcca054_0 conda-forge curl 7.71.1 he644dc0_8 conda-forge editdistance 0.6.2 py38h17151c0_2 conda-forge htslib 1.3.1 h18ffd7a_3 bioconda k8 1.2 h6618dc6_1 bioconda kernel-headers_linux-64 3.10.0 h4a8ded7_14 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge ld_impl_linux-64 2.40 hf3520f5_7 conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libcurl 7.71.1 hcdd3856_8 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h77fa898_10 conda-forge libgfortran-ng 13.2.0 h69a702a_10 conda-forge libgfortran5 13.2.0 h3d2ce59_10 conda-forge libgomp 13.2.0 h77fa898_10 conda-forge liblapack 3.9.0 22_linux64_openblas conda-forge libnghttp2 1.41.0 hab1572f_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 13.2.0 hc0a3c3a_10 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libzlib 1.2.13 h4ab18f5_6 conda-forge minimap2 2.28 he4a0461_1 bioconda ncurses 6.5 h59595ed_0 conda-forge numpy 1.24.4 py38h59b608b_0 conda-forge openssl 1.1.1w hd590300_0 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pysam 0.9.1 py38hd1a2d5f_10 bioconda python 3.8.15 h257c98d_0_cpython conda-forge python_abi 3.8 4_cp38 conda-forge readline 8.2 h8228510_1 conda-forge samtools 1.3.1 h80b0bb3_7 bioconda setuptools 70.0.0 pyhd8ed1ab_0 conda-forge sysroot_linux-64 2.17 h4a8ded7_14 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge wheel 0.43.0 pyhd8ed1ab_1 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 h4ab18f5_6 conda-forge ```

Some googling led me to this and this issues which led to the pysam release notes.

In the end creating a new environment with the following command solved the problem:

micromamba create -n FLAMES2 \
    "python>=3.7" samtools "pysam>=0.11.0" minimap2 numpy editdistance \
    -c bioconda -c conda-forge

Would be nice if dependencies were defined a little more clearly.