Merge branch 'refactor/rename_minos'

EI-CoreBioinformatics · May 22, 2020 · 2eec618 · 2eec618
2 parents 727b750 + f7e94c8
commit 2eec618
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diff --git a/bin/slurm/gmc_run_sub → bin/slurm/minos_run_sub b/bin/slurm/gmc_run_sub → bin/slurm/minos_run_sub
@@ -1,7 +1,7 @@
 #!/bin/bash
 
-app=gmc
-app_cmd=GMCRUN
+app=minos
+app_cmd=MINOS_RUN
 runmode=run
 
 # Check environment variable for the email address to which to send pipeline failure emails

diff --git a/build.sh b/build.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-install_prefix=/ei/software/cb/gmc
+install_prefix=/ei/software/cb/minos
 expected_version=$(grep -o "version *= *[\".0-9]\+" setup.py | sed "s/[\" ]//g" | cut -f 2 -d =)
 
 
@@ -27,5 +27,5 @@ echo "Installing to $install_prefix/$version"
 
 #rm dist/*whl
 python setup.py bdist_wheel
-pip install --prefix=${install_prefix}/${version}/x86_64 -U dist/gmc-${version}-*.whl
-#pip install --install-option="--prefix=/ei/software/testing/gmc/${version}/x86_64" -U dist/gmc-${version}-*.whl
+pip install --prefix=${install_prefix}/${version}/x86_64 -U dist/minos-${version}-*.whl
+#pip install --install-option="--prefix=/ei/software/testing/minos/${version}/x86_64" -U dist/minos-${version}-*.whl
diff --git a/eicore/snakemake_helper.py b/eicore/snakemake_helper.py
@@ -28,7 +28,7 @@ def get_etc_dir():
 
 ETC_DIR = get_etc_dir() 
 DEFAULT_HPC_CONFIG_FILE = os.path.join(ETC_DIR, "hpc_config.json")
-DEFAULT_CONFIG_FILE = os.path.join(ETC_DIR, "gmc_config.yaml")
+DEFAULT_CONFIG_FILE = os.path.join(ETC_DIR, "minos_config.yaml")
 
 @unique
 class RunMode(Enum):
@@ -218,7 +218,7 @@ def run_snakemake(snakefile, out_dir, cfg_file, exe_env, dryrun=False, unlock=Fa
 						printshellcmds=True,
 						printreason=True,
 						stats=os.path.join(out_dir, os.path.basename(snakefile) + "-" + NOW + ".stats"),
-						jobname="gmc.{rulename}.{jobid}",
+						jobname="minos.{rulename}.{jobid}",
 						force_incomplete=True,
 						# detailed_summary=args.detailed_summary,
 						# list_resources=True,

diff --git a/etc/Singularity.gmc.centos.def → etc/Singularity.minos.centos.def b/etc/Singularity.gmc.centos.def → etc/Singularity.minos.centos.def
diff --git a/etc/hpc_config.json b/etc/hpc_config.json
@@ -3,193 +3,193 @@
     "partition": "ei-medium",
     "memory": "8192",
     "cores": "8",
-    "J": "gmc",
+    "J": "minos",
     "time": "24:00:00",
     "exclude": "t128n84"
   },
-  "gmc_mikado_prepare": {
+  "minos_mikado_prepare": {
     "memory": "122880",
     "cores": "30",
-    "J": "gmc_mprep"
+    "J": "minos_mprep"
   },
-  "gmc_metrics_cpc2": {
+  "minos_metrics_cpc2": {
     "memory": "20480",
     "cores": "4",
-    "J": "gmc_met_cpc2"
+    "J": "minos_met_cpc2"
   },
-  "gmc_metrics_kallisto_index": {
+  "minos_metrics_kallisto_index": {
     "memory": "12288",
     "cores": "1",
-    "J": "gmc_met_kallisto_index"
+    "J": "minos_met_kallisto_index"
   },
-  "gmc_metrics_kallisto_quant": {
+  "minos_metrics_kallisto_quant": {
     "memory": "61440",
     "cores": "32",
-    "J": "gmc_met_kallisto_quant"
+    "J": "minos_met_kallisto_quant"
   },
-  "gmc_metrics_mikado_compare_vs_all": {
+  "minos_metrics_mikado_compare_vs_all": {
     "memory": "30720",
     "cores": "1",
-    "J": "gmc_met_mikado_compare_all"
+    "J": "minos_met_mikado_compare_all"
   },
-  "gmc_metrics_mikado_compare_vs_proteins": {
+  "minos_metrics_mikado_compare_vs_proteins": {
     "memory": "30720",
     "cores": "1",
-    "J": "gmc_met_mikado_cmp_prot"
+    "J": "minos_met_mikado_cmp_prot"
   },
-  "gmc_metrics_mikado_compare_vs_transcripts": {
+  "minos_metrics_mikado_compare_vs_transcripts": {
     "memory": "30720",
     "cores": "1",
-    "J": "gmc_met_mikado_cmp_tran"
+    "J": "minos_met_mikado_cmp_tran"
   },
-  "gmc_mikado_compare_index_reference": {
+  "minos_mikado_compare_index_reference": {
     "memory": "8192",
     "cores": "1",
-    "J": "gmc_mikado_cmp_index"
+    "J": "minos_mikado_cmp_index"
   },
-  "gmc_metrics_blastp_mkdb": {
+  "minos_metrics_blastp_mkdb": {
     "memory": "10240",
     "cores": "1",
-    "J": "gmc_met_makeblastdb"
+    "J": "minos_met_makeblastdb"
   },
-  "gmc_chunk_proteins": {
+  "minos_chunk_proteins": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_chunk_cds"
+    "J": "minos_chunk_cds"
   },
-  "gmc_gffread_extract_sequences": {
+  "minos_gffread_extract_sequences": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_generate_cds"
+    "J": "minos_generate_cds"
   },
-  "gmc_metrics_blastp_chunked": {
+  "minos_metrics_blastp_chunked": {
     "memory": "32768",
     "cores": "8",
-    "J": "gmc_met_blastp"
+    "J": "minos_met_blastp"
   },
-  "gmc_metrics_blastp_tophit": {
+  "minos_metrics_blastp_tophit": {
     "cores": "1",
     "memory": "4096",
-    "J": "gmc_met_blastp_tophit"
+    "J": "minos_met_blastp_tophit"
   },
-  "gmc_mikado_serialise": {
+  "minos_mikado_serialise": {
     "cores": "32",
     "memory": "125952",
-    "J": "gmc_mikado_serialise"
+    "J": "minos_mikado_serialise"
   },
-  "gmc_mikado_pick": {
+  "minos_mikado_pick": {
     "cores": "30",
     "memory": "125952",
-    "J": "gmc_mikado_pick"
+    "J": "minos_mikado_pick"
   },
-  "gmc_kallisto_index_post_pick": {
+  "minos_kallisto_index_post_pick": {
     "memory": "12288",
     "cores": "1",
-    "J": "gmc_met_kallisto_index_post_pick"
+    "J": "minos_met_kallisto_index_post_pick"
   },
-  "gmc_kallisto_quant_post_pick": {
+  "minos_kallisto_quant_post_pick": {
     "memory": "61440",
     "cores": "32",
-    "J": "gmc_met_kallisto_quant_post_pick"
+    "J": "minos_met_kallisto_quant_post_pick"
   },
-  "gmc_gff_validate_post_gt": {
+  "minos_gff_validate_post_gt": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_gff_validate_post_gt"
+    "J": "minos_gff_validate_post_gt"
   },
-  "gmc_collapse_metrics": {
+  "minos_collapse_metrics": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_collapse_metrics"
+    "J": "minos_collapse_metrics"
   },
-  "gmc_create_release_gffs": {
+  "minos_create_release_gffs": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_create_release_gffs"
+    "J": "minos_create_release_gffs"
   },
-  "gmc_sort_release_gffs": {
+  "minos_sort_release_gffs": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_sort_release_gffs"
+    "J": "minos_sort_release_gffs"
   },
-  "gmc_final_sanity_check": {
+  "minos_final_sanity_check": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_final_sanity_check"
+    "J": "minos_final_sanity_check"
   },
-  "gmc_generate_mikado_stats": {
+  "minos_generate_mikado_stats": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_generate_mikado_stats"
+    "J": "minos_generate_mikado_stats"
   },
-  "gmc_extract_final_sequences": {
+  "minos_extract_final_sequences": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_extract_final_sequences"
+    "J": "minos_extract_final_sequences"
   },
-  "gmc_extract_final_transcripts": {
+  "minos_extract_final_transcripts": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_extract_final_sequences"
+    "J": "minos_extract_final_sequences"
   },
-  "gmc_extract_final_proteins": {
+  "minos_extract_final_proteins": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_extract_final_proteins"
+    "J": "minos_extract_final_proteins"
   },
-  "gmc_cleanup_final_proteins": {
+  "minos_cleanup_final_proteins": {
     "memory": "2048",
     "cores": "1",
-    "J": "gmc_cleanup_final_proteins"
+    "J": "minos_cleanup_final_proteins"
   },
   "busco_proteins_prepare": {
     "memory": "8192",
     "cores": "8",
-    "J": "gmc_busco_proteins_prepare"
+    "J": "minos_busco_proteins_prepare"
   },
   "busco_proteins_final": {
     "memory": "8192",
     "cores": "8",
-    "J": "gmc_busco_proteins_final"
+    "J": "minos_busco_proteins_final"
   },
   "busco_transcripts_prepare": {
     "memory": "8192",
     "cores": "8",
-    "J": "gmc_busco_transcripts_prepare"
+    "J": "minos_busco_transcripts_prepare"
   },
   "busco_transcripts_final": {
     "memory": "8192",
     "cores": "8",
-    "J": "gmc_busco_transcripts_final"
+    "J": "minos_busco_transcripts_final"
   },
   "busco_genome": {
     "memory": "8192",
     "cores": "8",
-    "J": "gmc_busco_genome"
+    "J": "minos_busco_genome"
   },
-  "gmc_metrics_bedtools_repeat_coverage": {
+  "minos_metrics_bedtools_repeat_coverage": {
     "memory": "8192",
     "cores": "1",
-    "J": "gmc_metrics_bedtools_repeat_coverage"
+    "J": "minos_metrics_bedtools_repeat_coverage"
   },
-  "gmc_metrics_blastp_combine": {
+  "minos_metrics_blastp_combine": {
     "memory": "4096",
     "cores": "1",
-    "J": "gmc_metrics_blastp_combine"
+    "J": "minos_metrics_blastp_combine"
   },
-  "gmc_generate_final_table": {
+  "minos_generate_final_table": {
     "memory": "4096",
     "cores": "1",
-    "J": "gmc_generate_final_table"
+    "J": "minos_generate_final_table"
   },
-  "gmc_generate_tx2gene_maps": {
+  "minos_generate_tx2gene_maps": {
     "memory": "4096",
     "cores": "1",
-    "J": "gmc_generate_tx2gene_maps"
+    "J": "minos_generate_tx2gene_maps"
   },
-  "gmc_metrics_generate_metrics_matrix": {
+  "minos_metrics_generate_metrics_matrix": {
     "memory": "4096",
     "cores": "1",
-    "J": "gmc_metrics_generate_metrics_matrix"
+    "J": "minos_metrics_generate_metrics_matrix"
   }
 }
diff --git a/etc/gmc_config.yaml → etc/minos_config.yaml b/etc/gmc_config.yaml → etc/minos_config.yaml
@@ -42,16 +42,16 @@ misc:
 
 program_calls:
   mikado: "singularity exec {container} mikado {program}"
-  gffread: "singularity exec /ei/software/cb/containers/gmc/x86_64/Singularity.img gffread"
-  cpc2: "singularity exec /ei/software/cb/containers/gmc/x86_64/Singularity.img CPC2.py"
-  kallisto: "singularity exec /ei/software/cb/containers/gmc/x86_64/Singularity.img kallisto {program}"
-  blast: "singularity exec /ei/software/cb/containers/gmc/x86_64/Singularity.img {program}"
-  genometools: "singularity exec /ei/software/cb/containers/gmc/x86_64/Singularity.img gt"
-  prinseq: "singularity exec /ei/software/cb/containers/gmc/x86_64/Singularity.img prinseq-lite.pl"
-  busco: "singularity exec /ei/software/cb/containers/gmc/x86_64/Singularity.busco.img busco"
-  copy: "singularity exec /ei/software/cb/containers/gmc/x86_64/Singularity.busco.img cp -r"
+  gffread: "singularity exec /ei/software/cb/containers/minos/x86_64/Singularity.img gffread"
+  cpc2: "singularity exec /ei/software/cb/containers/minos/x86_64/Singularity.img CPC2.py"
+  kallisto: "singularity exec /ei/software/cb/containers/minos/x86_64/Singularity.img kallisto {program}"
+  blast: "singularity exec /ei/software/cb/containers/minos/x86_64/Singularity.img {program}"
+  genometools: "singularity exec /ei/software/cb/containers/minos/x86_64/Singularity.img gt"
+  prinseq: "singularity exec /ei/software/cb/containers/minos/x86_64/Singularity.img prinseq-lite.pl"
+  busco: "singularity exec /ei/software/cb/containers/minos/x86_64/Singularity.busco.img busco"
+  copy: "singularity exec /ei/software/cb/containers/minos/x86_64/Singularity.busco.img cp -r"
   bedtools:
-    coverageBed: "singularity exec /ei/software/cb/containers/gmc/x86_64/Singularity.img coverageBed"
+    coverageBed: "singularity exec /ei/software/cb/containers/minos/x86_64/Singularity.img coverageBed"
   time: "/usr/bin/time -v"
 
 collapse_metrics_thresholds:

diff --git a/etc/scoring_template.yaml b/etc/scoring_template.yaml
@@ -25,7 +25,7 @@ as_requirements:
     max_exon_length: {operator: le, value: 10000}
 not_fragmentary:
   # expression: [combined_cds_length]
-  ### GMC:GENERATE_NF_EXPRESSION
+  ### MINOS:GENERATE_NF_EXPRESSION
   ### DO NOT MODIFY THIS OR PRECEDING LINE
   parameters:
     # is_complete: {operator: eq, value: true}
@@ -35,11 +35,11 @@ not_fragmentary:
     exon_num.mono: {operator: eq, value: 1}
     combined_cds_length.mono: {operator: gt, value: 300}
     # combined_cds_length: {operator: gt, value: 300}
-    ### GMC:GENERATE_NF_PARAMS
+    ### MINOS:GENERATE_NF_PARAMS
     ### DO NOT MODIFY THIS OR PRECEDING LINE
 scoring:
   # external metrics START
-  ### GMC:GENERATE_EXTERNAL_SCORING
+  ### MINOS:GENERATE_EXTERNAL_SCORING
   ### DO NOT MODIFY THIS OR PRECEDING LINE
   # external metrics END
   # internal metrics START

diff --git a/gmc/__init__.py → minos/__init__.py b/gmc/__init__.py → minos/__init__.py
@@ -1,9 +1,9 @@
 import pkg_resources
 
-__title__ = "gmc"
-__author__ = "Christian Schudoma (cschu)"
+__title__ = "minos"
+__author__ = "Christian Schudoma (cschu), Gemy Kaithakottil"
 __email__ = "christian.schudoma@earlham.ac.uk"
 __license__ = "MIT"
 __copyright__ = "Copyright 2019-2020 Earlham Institute"
-__version__ = pkg_resources.require("gmc")[0].version
+__version__ = pkg_resources.require("minos")[0].version