NGLess 1.4.1 → 1.4.1.1
raw patch · 6 files changed
+931/−2 lines, 6 filesbinary-added
Files
- Makefile +59/−0
- NGLess.cabal +5/−1
- NGLess/Version.hs +1/−1
- test_samples/data_set_repeated.fq +864/−0
- test_samples/sample.sam.gz binary
- test_samples/very_short.gtf +2/−0
+ Makefile view
@@ -0,0 +1,59 @@+VERSION := $(shell ./build-scripts/read-version.sh)+progname := ngless+distdir := ngless-${VERSION}++prefix=/usr/local+deps=$(prefix)/share/$(progname)+exec=$(prefix)/bin++all: ngless++ngless:+ stack build $(STACKOPTS)++modules:+ cd Modules && $(MAKE)++static:+ stack build $(STACKOPTS) --ghc-options='-fPIC' --force-dirty --flag NGLess:static++fast:+ stack build --fast --work-dir .stack-work-fast $(STACKOPTS)++check:+ stack test --work-dir .stack-work-check $(STACKOPTS)++fastcheck:+ stack test --fast --work-dir .stack-work-fastcheck $(STACKOPTS)++dist: ngless-${VERSION}.tar.gz++# Synonym+tests: check++all_tests: check+ PATH=$(stack path --bin-path):${PATH} ./run-tests.sh++bench:+ stack bench --work-dir .stack-work-bench $(STACKOPTS)++profile:+ stack build $(STACKOPTS) --executable-profiling --library-profiling --ghc-options="-fprof-auto -rtsopts"++install: ngless $(MEGAHIT_BINS)+ mkdir -p $(exec)+ mkdir -p $(deps)/bin+ stack --local-bin-path $(exec) install $(STACKOPTS)++clean:+ stack clean $(STACKOPTS)++distclean: clean++ngless-${VERSION}.tar.gz: ngless+ mkdir -p $(distdir)/share $(distdir)/bin+ stack build $(STACKOPTS)+ cp dist/build/$(progname)/$(progname) $(distdir)/bin+ rm -rf $(distdir)++.PHONY: all build clean check tests all_tests distclean dist static fast fastcheck modules
NGLess.cabal view
@@ -5,7 +5,7 @@ -- see: https://github.com/sol/hpack name: NGLess-version: 1.4.1+version: 1.4.1.1 synopsis: NGLess implements ngless, a DSL for processing sequencing data description: NGLess implements a domain-specific language for processing next generation data, particularly metagenomics. category: Domain Specific Language@@ -25,6 +25,10 @@ Html/nglessQC.html Html/perBaseQualScores.css NGLess/Interpretation/Count/RefSeqInfoVector.h+ test_samples/sample.sam.gz+ test_samples/data_set_repeated.fq+ test_samples/very_short.gtf+ Makefile source-repository head type: git
NGLess/Version.hs view
@@ -14,7 +14,7 @@ import Paths_NGLess (version) versionStr :: String-versionStr = showVersion version+versionStr = "1.4.1" versionStrLong :: String versionStrLong = "1.4.1"
+ test_samples/data_set_repeated.fq view
@@ -0,0 +1,864 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0/2+aabbbaaaababb`baaaaaaaaaaa``a```aaaa+@IRIS:7:1:22:453#0/2+TGGGGGATTCCATCCACAAACGCAAAGTTTATGGCT++IRIS:7:1:22:453#0/2+abbbbbaabaabaaababaaabaaa`b^aaa`aaa]+@IRIS:7:1:22:1371#0/2+TTTTTGGGGCGATTCCACCGGGAATTGGGAAAATAA++IRIS:7:1:22:1371#0/2+aabbaQ_b^BBBBBBBBBBBBBBBBBBBBBBBBBBB
+ test_samples/sample.sam.gz view
binary file changed (absent → 577424 bytes)
+ test_samples/very_short.gtf view
@@ -0,0 +1,2 @@+X protein_coding gene 119 721 . + . gene_id "WBGene00010199"; gene_name "bet-2"; gene_source "ensembl"; gene_biotype "protein_coding";+X ncRNA gene 305 415 . - . gene_id "WBGene00199555"; gene_name "F57C7.11"; gene_source "ensembl"; gene_biotype "ncRNA";