adding freebayes version 1.3.8 attempt 2

[erinyoung]

Attempt #2 to close #1057

There is a new version of freebayes. I attempted to create a dockerfile for this new version in #975, but was unsuccessful.

It was suggested that I attempt installing from conda. This is my attempt at use micromamba's verion 1.5.8 base with the corresponding error.

0.529 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.109.133, ...
0.538 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
0.556 HTTP request sent, awaiting response... 200 OK
0.573 Length: 30414 (30K) [text/plain]
0.573 Saving to: ‘SARS-CoV-2.reference.fasta’
0.573 
0.573      0K .......... .......... .........                       100% 16.1M=0.002s
0.575 
0.575 2024-12-23 18:21:40 (16.1 MB/s) - ‘SARS-CoV-2.reference.fasta’ saved [30414/30414]
0.575 
0.580 index file SARS-CoV-2.reference.fasta.fai not found, generating...
0.599 /opt/conda/conda-bld/freebayes_1711687983774/_build_env/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/stl_vector.h:1123: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator<Allele*>; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.
0.600 bash: line 1:    27 Aborted                 freebayes -f SARS-CoV-2.reference.fasta SRR13957123.sorted.bam > var.vcf
------
Dockerfile:48
--------------------
  47 |     
  48 | >>> RUN wget https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123.sorted.bam && \
  49 | >>>     wget https://raw.githubusercontent.com/artic-network/primer-schemes/refs/heads/master/nCoV-2019/V5.3.2/SARS-CoV-2.reference.fasta && \
  50 | >>>     freebayes -f SARS-CoV-2.reference.fasta SRR13957123.sorted.bam > var.vcf && \
  51 | >>>     head var.vcf
  52 |     
--------------------
ERROR: failed to solve: process "/usr/local/bin/_dockerfile_shell.sh wget https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123.sorted.bam &&     wget https://raw.githubusercontent.com/artic-network/primer-schemes/refs/heads/master/nCoV-2019/V5.3.2/SARS-CoV-2.reference.fasta &&     freebayes -f SARS-CoV-2.reference.fasta SRR13957123.sorted.bam > var.vcf &&     head var.vcf" did not complete successfully: exit code: 134

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