From 06406ff30ccd6d142cdc4f548279d98a9cd85e15 Mon Sep 17 00:00:00 2001 From: Aaron Wagen <65199038+aaronwagen@users.noreply.github.com> Date: Thu, 15 Jan 2026 17:00:51 +0000 Subject: [PATCH 1/7] Add pysam samtools python polars --- combinations/hash.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 632b4d954..3680217ae 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -932,3 +932,4 @@ bwa=0.7.19,samtools=1.22 montreal-forced-aligner=3.3.8 samtools=1.17,bam-readcount=1.0.1 libcarna-python=0.2.0,numpy=1.26.4,ffmpeg=4.3.2,giatools=0.7.3,ome-zarr=0.12.2,pandas=2.3.3 quay.io/bioconda/base-glibc-debian-bash:latest 0 +htslib=1.18=h81da01d_0,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* From e57886f99ee211198cc28067cb0ebe4358c69320 Mon Sep 17 00:00:00 2001 From: Aaron Wagen <65199038+aaronwagen@users.noreply.github.com> Date: Thu, 15 Jan 2026 17:33:48 +0000 Subject: [PATCH 2/7] Add samtools pysam polars htslib From 74c62344b0dee406f32fe7cb20b5752a450753c2 Mon Sep 17 00:00:00 2001 From: Aaron Wagen <65199038+aaronwagen@users.noreply.github.com> Date: Thu, 15 Jan 2026 17:40:04 +0000 Subject: [PATCH 3/7] mulled-v2-b8df37f6e23fbd37c538c5e890f2106af1ba56c7:c5058af96085e7aa8ea109fc13882ce93a4d70c5 htslib=1.18=h81da01d_0,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* --- combinations/hash.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 3680217ae..d98b17329 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -933,3 +933,4 @@ montreal-forced-aligner=3.3.8 samtools=1.17,bam-readcount=1.0.1 libcarna-python=0.2.0,numpy=1.26.4,ffmpeg=4.3.2,giatools=0.7.3,ome-zarr=0.12.2,pandas=2.3.3 quay.io/bioconda/base-glibc-debian-bash:latest 0 htslib=1.18=h81da01d_0,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* + From c935d03584264247df73a5e2710328914b08d80d Mon Sep 17 00:00:00 2001 From: Aaron Wagen <65199038+aaronwagen@users.noreply.github.com> Date: Thu, 15 Jan 2026 17:47:12 +0000 Subject: [PATCH 4/7] mulled-v2-de7cc1534872d757f77d2e5dfb47f5141b4d6381:6330bee9b98441c0ccf35929ab85705924749400 htslib=1.18=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* --- combinations/hash.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index d98b17329..2cc36b0e2 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -933,4 +933,5 @@ montreal-forced-aligner=3.3.8 samtools=1.17,bam-readcount=1.0.1 libcarna-python=0.2.0,numpy=1.26.4,ffmpeg=4.3.2,giatools=0.7.3,ome-zarr=0.12.2,pandas=2.3.3 quay.io/bioconda/base-glibc-debian-bash:latest 0 htslib=1.18=h81da01d_0,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* +htslib=1.18=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* From 010c20b524e9f97cfd3a6f1892c83f2af9e68b2d Mon Sep 17 00:00:00 2001 From: Aaron Wagen <65199038+aaronwagen@users.noreply.github.com> Date: Thu, 15 Jan 2026 17:52:08 +0000 Subject: [PATCH 5/7] mulled-v2-de7cc1534872d757f77d2e5dfb47f5141b4d6381:6330bee9b98441c0ccf35929ab85705924749400 htslib=1.18=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1 --- combinations/hash.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 2cc36b0e2..640b085fa 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -933,5 +933,5 @@ montreal-forced-aligner=3.3.8 samtools=1.17,bam-readcount=1.0.1 libcarna-python=0.2.0,numpy=1.26.4,ffmpeg=4.3.2,giatools=0.7.3,ome-zarr=0.12.2,pandas=2.3.3 quay.io/bioconda/base-glibc-debian-bash:latest 0 htslib=1.18=h81da01d_0,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* -htslib=1.18=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* +htslib=1.18=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1 From 608448642e1e0d9d8238755969183f60ba9f8843 Mon Sep 17 00:00:00 2001 From: Aaron Wagen <65199038+aaronwagen@users.noreply.github.com> Date: Thu, 15 Jan 2026 21:59:04 +0000 Subject: [PATCH 6/7] htslib=1.19=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1 --- combinations/hash.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 640b085fa..d5d21e5da 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -933,5 +933,5 @@ montreal-forced-aligner=3.3.8 samtools=1.17,bam-readcount=1.0.1 libcarna-python=0.2.0,numpy=1.26.4,ffmpeg=4.3.2,giatools=0.7.3,ome-zarr=0.12.2,pandas=2.3.3 quay.io/bioconda/base-glibc-debian-bash:latest 0 htslib=1.18=h81da01d_0,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* -htslib=1.18=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1 +htslib=1.19=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1 From 6d636cdbedc1f84d060727c574d461a5532f73cf Mon Sep 17 00:00:00 2001 From: Aaron Wagen <65199038+aaronwagen@users.noreply.github.com> Date: Thu, 15 Jan 2026 22:00:46 +0000 Subject: [PATCH 7/7] htslib=1.19=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1 --- combinations/hash.tsv | 1 - 1 file changed, 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index d5d21e5da..845f79be0 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -932,6 +932,5 @@ bwa=0.7.19,samtools=1.22 montreal-forced-aligner=3.3.8 samtools=1.17,bam-readcount=1.0.1 libcarna-python=0.2.0,numpy=1.26.4,ffmpeg=4.3.2,giatools=0.7.3,ome-zarr=0.12.2,pandas=2.3.3 quay.io/bioconda/base-glibc-debian-bash:latest 0 -htslib=1.18=h81da01d_0,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1,python=3.10.* htslib=1.19=h81da01d_0,polars=0.18.15,pysam=0.23.3=py310h64e62c9_1,samtools=1.18=h50ea8bc_1