From 2792b5fefebde60f55e7b0613ec17d4818f94edc Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 22 Jul 2024 09:31:53 +1000 Subject: [PATCH 1/6] macros --- tools/dorado/macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/dorado/macros.xml b/tools/dorado/macros.xml index 38fc7b1a..e3d5e31f 100644 --- a/tools/dorado/macros.xml +++ b/tools/dorado/macros.xml @@ -1,6 +1,6 @@ - 0.7.1+80da5f5 + 0.7.2+9ac85c6 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 From 683e4f0ab8122dc92c48fbe7d32d5460a9d33a3d Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 22 Jul 2024 09:37:42 +1000 Subject: [PATCH 2/6] loc file --- .../dorado/tool-data/dorado_models.loc.sample | 117 +++++++++--------- 1 file changed, 59 insertions(+), 58 deletions(-) diff --git a/tools/dorado/tool-data/dorado_models.loc.sample b/tools/dorado/tool-data/dorado_models.loc.sample index e84d214e..57207bbf 100644 --- a/tools/dorado/tool-data/dorado_models.loc.sample +++ 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58b978562389bd0f1842601fb83cdf1eb2920218 rna004_130bps_sup@v5.0.0 /models/rna004_130bps_sup@v5.0.0 +58b978562389bd0f1842601fb83cdf1eb2920218_rna004_130bps_sup@v5.0.0_m6A@v1 58b978562389bd0f1842601fb83cdf1eb2920218 rna004_130bps_sup@v5.0.0_m6A@v1 /models/rna004_130bps_sup@v5.0.0_m6A@v1 +58b978562389bd0f1842601fb83cdf1eb2920218_rna004_130bps_sup@v5.0.0_pseU@v1 58b978562389bd0f1842601fb83cdf1eb2920218 rna004_130bps_sup@v5.0.0_pseU@v1 /models/rna004_130bps_sup@v5.0.0_pseU@v1 From 7b48b4143cf311555160391a6f8c5c878aff2747 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 22 Jul 2024 09:41:44 +1000 Subject: [PATCH 3/6] try testing --- tools/dorado/README.md | 6 +++--- tools/dorado/dorado.xml | 8 +++----- tools/dorado/dorado_pod5_convert.xml | 8 +++----- 3 files changed, 9 insertions(+), 13 deletions(-) diff --git a/tools/dorado/README.md b/tools/dorado/README.md index 218e90f9..2cfa6f39 100644 --- a/tools/dorado/README.md +++ b/tools/dorado/README.md @@ -25,8 +25,8 @@ To update the list, modify `tool-data/dorado_models.loc.sample`. Because models can be added and removed, models are listed **per container** in the loc file. -Here's some code to **append** the models from the container with hash -`1c65eb070a9fc1d88710c4dc09b06541f96fdd28` to the loc file. +Here's some code to update the loc file with models from the container with hash +`1c65eb070a9fc1d88710c4dc09b06541f96fdd28`. ```bash export DORADO_HASH="1c65eb070a9fc1d88710c4dc09b06541f96fdd28" @@ -34,7 +34,7 @@ export DORADO_HASH="1c65eb070a9fc1d88710c4dc09b06541f96fdd28" apptainer exec "docker://nanoporetech/dorado:sha${DORADO_HASH}" \ ls /models | \ awk -v hash="${DORADO_HASH}" '{print hash "_" $0 "\t" hash "\t" $0 "\t/models/" $0}' \ - >> tool-data/dorado_models.loc.sample + > tool-data/dorado_models.loc.sample ``` The loc file doesn't have a header, so you can keep it sorted. diff --git a/tools/dorado/dorado.xml b/tools/dorado/dorado.xml index aee04635..96279282 100644 --- a/tools/dorado/dorado.xml +++ b/tools/dorado/dorado.xml @@ -1,4 +1,4 @@ - + basecaller for raw Oxford Nanopore data macros.xml @@ -28,9 +28,7 @@ calls.bam ]]> - - + @@ -134,7 +132,7 @@ calls.bam - + diff --git a/tools/dorado/dorado_pod5_convert.xml b/tools/dorado/dorado_pod5_convert.xml index a7a21d39..592ac82a 100644 --- a/tools/dorado/dorado_pod5_convert.xml +++ b/tools/dorado/dorado_pod5_convert.xml @@ -1,4 +1,4 @@ - + converter for raw Oxford Nanopore data macros.xml @@ -27,9 +27,7 @@ input_fast5 - - + @@ -42,7 +40,7 @@ input_fast5 - + From 9e2ada96c4f34aef27704c918dd40385727b8fc3 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 22 Jul 2024 10:48:55 +1000 Subject: [PATCH 4/6] profile --- tools/dorado/dorado.xml | 2 +- tools/dorado/dorado_pod5_convert.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/dorado/dorado.xml b/tools/dorado/dorado.xml index 96279282..777db836 100644 --- a/tools/dorado/dorado.xml +++ b/tools/dorado/dorado.xml @@ -1,4 +1,4 @@ - + basecaller for raw Oxford Nanopore data macros.xml diff --git a/tools/dorado/dorado_pod5_convert.xml b/tools/dorado/dorado_pod5_convert.xml index 592ac82a..31af8e7d 100644 --- a/tools/dorado/dorado_pod5_convert.xml +++ b/tools/dorado/dorado_pod5_convert.xml @@ -1,4 +1,4 @@ - + converter for raw Oxford Nanopore data macros.xml From 822ab8614aa7b0b6634593f990c6d214fc658aae Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 22 Jul 2024 11:02:27 +1000 Subject: [PATCH 5/6] profile --- tools/dorado/macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/dorado/macros.xml b/tools/dorado/macros.xml index e3d5e31f..d0ac08fb 100644 --- a/tools/dorado/macros.xml +++ b/tools/dorado/macros.xml @@ -1,7 +1,7 @@ 0.7.2+9ac85c6 - 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 + 58b978562389bd0f1842601fb83cdf1eb2920218 nanoporetech/dorado:sha@CONTAINER_HASH@ From 3f7d25491f172cd7acd3cd5a517018544ad13baf Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 22 Jul 2024 11:09:13 +1000 Subject: [PATCH 6/6] datatype --- tools/dorado/dorado_pod5_convert.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/dorado/dorado_pod5_convert.xml b/tools/dorado/dorado_pod5_convert.xml index 31af8e7d..75afad36 100644 --- a/tools/dorado/dorado_pod5_convert.xml +++ b/tools/dorado/dorado_pod5_convert.xml @@ -32,7 +32,7 @@ input_fast5 - +