Update ubuntu-22.04-cxx-clang images

paulsengroup · Jan 29, 2024 · ba3c344 · ba3c344
1 parent af1855f
commit ba3c344
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Showing 8 changed files with 27 additions and 24 deletions.
diff --git a/benchmarks/configs/benchmark_cool2hic.config b/benchmarks/configs/benchmark_cool2hic.config
@@ -9,7 +9,9 @@ params {
 
     // mcool_file = "${data_dir}/ENCFF447ERX.mcool"
     mcool_file = "/dev/shm/2023-hictk-paper/ENCFF447ERX.mcool"
+
     replicates = 3
+    resolutions = [10, 100, 500, 1000, 5000, 10000, 25000, 50000, 100000, 250000, 500000, 1000000, 2500000]
 }
 
 process {
@@ -20,6 +22,6 @@ process {
         container = 'ghcr.io/paulsengroup/2023-hictk-paper/plotting:1.0.0'
     }
     withName:hictk_convert {
-        memory = 650.GB
+        memory = 24.GB
     }
 }
diff --git a/benchmarks/workflows/benchmark_cool2hic.nf b/benchmarks/workflows/benchmark_cool2hic.nf
@@ -8,9 +8,11 @@ nextflow.enable.dsl=2
 workflow {
     Channel.fromPath(params.mcool_file, checkIfExists: true).set { mcool }
 
+    Channel.of(params.resolutions).flatten().set { resolutions }
     task_ids = Channel.of((1..params.replicates).toList()).flatten()
 
     task_ids.combine(mcool)
+        .combine(resolutions)
         .set { tasks }
 
     hictk_convert(
@@ -23,41 +25,40 @@ workflow {
 }
 
 
-process hictk_convert {
+process hictk_convert_sc {
     publishDir "${params.outdir}/hictk/", mode: 'copy'
 
-    cpus 4
+    cpus 1
 
-    tag "${mcool.fileName}_${id}"
+    tag "${mcool.fileName}_${resolution}_${id}"
 
     input:
         tuple val(id),
-              path(mcool)
+              path(mcool),
+              val(resolution)
 
     output:
         tuple val(id),
+              val(resolution),
               path("*.tsv"), emit: tsv
 
     shell:
-        outname="${id}__${mcool.simpleName}__hictk.tsv"
-        memory_gb=task.memory.toGiga()
+        outname="${id}__${mcool.simpleName}__hictk__${resolution}.tsv"
         '''
         set -o pipefail
 
-        printf 'tool\\tformat\\tresolution\\ttime\\tmemory\\n' > '!{outname}'
-        printf 'hictk\\tcooler\\tall\\t' >> '!{outname}'
+        printf 'tool\\tformat\\tresolution\\tcpus\\ttime\\tmemory\\n' > '!{outname}'
+        printf 'hictk\\tcooler\\t!{resolution}\\t!{task.cpus}\\t' >> '!{outname}'
 
 
         mkdir tmp/
-        command time -f '%e\\t%M'                              \\
-                     -o '!{outname}'                           \\
-                     -a                                        \\
-            hictk convert '!{mcool}'                           \\
-                          out.hic                              \\
-                          --tmpdir tmp/                        \\
-                          --juicer-tools-jar "$HICTOOLS_JAR"   \\
-                          --juicer-tools-memory !{memory_gb}GB \\
-                          -p '!{task.cpus}'
+        command time -f '%e\\t%M'                                \\
+                     -o '!{outname}'                             \\
+                     -a                                          \\
+            hictk convert '!{mcool}::/resolutions/!{resolution}' \\
+                          out.hic                                \\
+                          --tmpdir tmp/                          \\
+                          -t '!{task.cpus}'
         '''
 }
 

diff --git a/containers/fetch-and-sum-bench__v1.0.0.Dockerfile b/containers/fetch-and-sum-bench__v1.0.0.Dockerfile
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 
-FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-15:20230707 as builder
+FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-17:20240126 as builder
 
 COPY conanfile.txt /tmp/
 RUN conan install /tmp/conanfile.txt             \

diff --git a/containers/hic-tools__v3.30.00.Dockerfile b/containers/hic-tools__v3.30.00.Dockerfile
@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: MIT
 
-FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-15:20230707 as builder
+FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-17:20240126 as builder
 
 COPY utils /tmp/utils
 

diff --git a/containers/hicrep__v0.2.6.Dockerfile b/containers/hicrep__v0.2.6.Dockerfile
@@ -17,7 +17,7 @@ RUN apt-get update \
 
 RUN /opt/hicrep/vanilla/bin/hicrep --help
 
-FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-15:20230707 as hicrep_hictk
+FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-17:20240126 as hicrep_hictk
 
 
 ARG HICREP_GIT='https://github.com/robomics/hicrep.git'

diff --git a/containers/juicer-tools__v1.22.01.Dockerfile b/containers/juicer-tools__v1.22.01.Dockerfile
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 
-FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-15:20230707 as builder
+FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-17:20240126 as builder
 
 COPY utils /tmp/utils
 

diff --git a/containers/possum__v0.0.1.Dockerfile b/containers/possum__v0.0.1.Dockerfile
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 
-FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-15:20230707 as builder
+FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-17:20240126 as builder
 
 ARG POSSUM_GIT='https://github.com/robomics/EigenVector.git'
 ARG POSSUM_PATCHED_TAG='eba7fb5be7dc14da2f56cb2894a3f14339c43a7e'

diff --git a/containers/straw-bench__v1.0.0.Dockerfile b/containers/straw-bench__v1.0.0.Dockerfile
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 
-FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-15:20230707 as builder
+FROM ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-17:20240126 as builder
 
 ARG STRAW_GIT='https://github.com/aidenlab/straw.git'
 ARG STRAW_GIT_TAG='2525edc29bbb48463799cad94cbd6e5e810210a0'