21543: Move Go code into go-lightning subdir.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/.licenseignore b/.licenseignore
index 0d77b26cc448356494453a417b0bbfa4c6d3531e..752f7f8f7ea1fb28daab61f39c8597ad4308b6af 100644 (file)
--- a/.licenseignore
+++ b/.licenseignore
@@ -1,6 +1,6 @@
 .licenseignore
 AUTHORS
-go.mod
-go.sum
-testdata/*
+go-lightning/go.mod
+go-lightning/go.sum
+go-lightning/testdata/*
 readme.md

diff --git a/docker/lightning/Dockerfile b/docker/lightning/Dockerfile
index a6df7bb3d3141a0322d1cc40c8f594b0120df8b8..7175ffc33b2eee57b171abbd418ed5e5c0daf7ab 100644 (file)
--- a/docker/lightning/Dockerfile
+++ b/docker/lightning/Dockerfile
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: AGPL-3.0
 
 # build instruction:
-# docker build -t dockername --file=/path/to/lightning/docker/lightning/Dockerfile /path/to/lightning
+# docker build -t dockername --file=/path/to/lightning/docker/lightning/Dockerfile /path/to/lightning/go-lightning
 
 FROM python:3.11-buster
 USER root
@@ -26,8 +26,8 @@ RUN apt-get install -qy --no-install-recommends wget \
 
 RUN pip install --upgrade pip matplotlib numpy pandas scikit-learn scipy
 
-RUN wget --progress=dot:giga https://go.dev/dl/go1.20.10.linux-amd64.tar.gz && \
-    tar -C /usr/local -xzf go1.20.10.linux-amd64.tar.gz
+RUN wget --progress=dot:giga https://go.dev/dl/go1.22.2.linux-amd64.tar.gz && \
+    tar -C /usr/local -xzf go1.22.2.linux-amd64.tar.gz
 
 ENV PATH $PATH:/usr/local/go/bin:/root/go/bin
 

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
deleted file mode 100755 (executable)
index c60e8fc..0000000
--- a/example-su92l-1kg.sh
+++ /dev/null
@@ -1,93 +0,0 @@
-#!/bin/bash
-
-set -ex
-
-PATH="${GOPATH:-${HOME}/go}/bin:${PATH}"
-go install
-lightning build-docker-image
-arv keep docker lightning-runtime
-
-priority=501
-project=su92l-j7d0g-jzei0m9yvgauhjf
-ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
-ref37_fa=su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz
-gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
-info=su92l-4zz18-ykpcoea5nisz74f
-tagset=su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz
-
-genome=$(lightning     ref2genome   -project ${project} -priority ${priority} -ref ${ref_fa})                                                          ; echo genome=${genome}
-fasta=$(lightning      vcf2fasta    -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})                     ; echo fasta=${fasta}
-# fasta=su92l-4zz18-9nq05jifgz7iult
-
-ref37_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles=true ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
-# ref37_lib=su92l-4zz18-vnhlv3g6yp1azls/library.gob
-# 539s
-# ref37_lib=su92l-4zz18-v0xfm2o1tu3u1w3/library.gob.gz
-# 2751s @ 4a3899f
-
-ref38_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles=true ${ref_fa}) ; echo ref38_lib=${ref38_lib}
-# ref38_lib=su92l-4zz18-swebknshfwsvys6/library.gob
-
-bed37=$(lightning export       -project ${project} -priority ${priority} -i ${ref37_lib} -output-format hgvs -ref /mnt/$ref37_fa -output-bed hg37.bed) ; echo bed37=${bed37}
-# bed37=su92l-4zz18-gb3hihiiaz0xaz9/export.csv
-# 463s @ 870319f
-bed38=$(lightning export       -project ${project} -priority ${priority} -i ${ref38_lib} -output-format hgvs -ref /mnt/$ref_fa -output-bed hg38.bed) ; echo bed38=${bed38}
-
-unfiltered=$(lightning import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true ${fasta})       ; echo unfiltered=${unfiltered}
-# unfiltered=su92l-4zz18-mz3546bib6oj1gg/library.gob
-# unfiltered=su92l-4zz18-72ovi5qrderxudv/library.gob
-# 24674s @ pre-38e6e7c
-# unfiltered=su92l-4zz18-ywhkc1hgdzxwp5u/library.gob
-# 18497s @ 64vcpu bf0968a
-# _____s @ 32vcpu 83983ad
-
-
-merged=$(lightning     merge        -project ${project} -priority ${priority} ${unfiltered} ${ref37_lib})                                              ; echo merged=${merged}
-# merged=su92l-4zz18-svw5xqe5g0ct2v1/library.gob
-# 2400s
-
-exportvcf=$(lightning  export       -project ${project} -priority ${priority} -i ${merged} -output-format vcf -ref /mnt/su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz -output-bed export.bed) ; echo exportvcf=${exportvcf}
-# exportvcf=su92l-4zz18-gz4svr6zyvipueu/export.csv
-# 5506s
-
-exporthgvs=$(lightning export       -project ${project} -priority ${priority} -i ${merged38} -output-format hgvs -ref /mnt/su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz -output-bed hg38.bed) ; echo exporthgvs=${exporthgvs}
-# 
-# 
-
-stats=$(lightning      stats        -project ${project} -priority ${priority} -i ${merged})                                                            ; echo stats=${stats}
-
-filtered=$(lightning   filter       -project ${project} -priority ${priority} -i ${merged} -min-coverage "0.9" -max-variants "30")                     ; echo filtered=${filtered}
-
-annotations=$(lightning annotate    -project ${project} -priority ${priority} -i ${merged})                                                            ; echo annotations=${annotations}
-
-pca=$(lightning        pca-go       -project ${project} -priority ${priority} -i ${unfiltered} -min-coverage "0.9" -max-variants "30")                 ; echo pca=${pca}
-# pca=su92l-4zz18-e3xhi2mzp8rqevd/pca.npy
-# 3987s @ c237c16
-plot=$(lightning       plot         -project ${project} -priority ${priority} -i ${pca} -labels-csv ${info}/sample_info.csv -sample-fasta-dir ${fasta})
-echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
-echo ${plot%%/*}
-# plot=su92l-4zz18-xyei3lnyxmgo7lh/plot.png
-# 535s @ c237c16
-
-merged38=$(lightning   merge        -project ${project} -priority ${priority} ${unfiltered} ${ref38_lib})                                              ; echo merged38=${merged38}
-# merged38=su92l-4zz18-xq17gtaltjxbm3n/library.gob
-# 1602s
-# merged38=su92l-4zz18-5kcaci3hqzukjv2/library.gob
-# 2815s @ 83983ad
-# merged38=su92l-4zz18-nq8dmtng68ozovu/library.gob.gz
-# 9803s @ 69b71af
-
-numpy=$(lightning      export-numpy -project ${project} -priority ${priority} -i ${merged38})                                                          ; echo numpy=${numpy}
-# numpy=su92l-4zz18-w3dx5k79mtbz6qt/matrix.npy
-# 6155s
-# numpy=su92l-4zz18-g1y2eg9qvngvkkq/matrix.npy
-# 6633s @ 83983ad
-# numpy=su92l-4zz18-cpw0i3z7wery77o/matrix.npy
-# 6311s @ 4e6ada0
-# numpy=su92l-4zz18-hljgbqs6c87wles/matrix.npy
-# 6824s @ 2e1cb2e
-# numpy=su92l-4zz18-vw31l0qzenyb44l/matrix.npy
-# 7403s @ 6785271
-# pcapy=$(lightning      pca          -project ${project} -priority ${priority} -i ${numpy})                                                             ; echo pcapy=${pcapy}
-comvar=$(lightning     numpy-comvar -project ${project} -priority ${priority} -i ${numpy} -annotations ${numpy%/matrix.npy}/annotations.tsv)           ; echo comvar=${comvar}
-# comvar=su92l-4zz18-s1yhngobdvcoc2e/commonvariants.csv

diff --git a/Makefile b/go-lightning/Makefile
similarity index 100%
rename from Makefile
rename to go-lightning/Makefile

diff --git a/anno2vcf.go b/go-lightning/anno2vcf.go
similarity index 100%
rename from anno2vcf.go
rename to go-lightning/anno2vcf.go

diff --git a/annotate.go b/go-lightning/annotate.go
similarity index 99%
rename from annotate.go
rename to go-lightning/annotate.go
index 00f1cad1556147c2b2ba31f2e8e3b4483ad02e20..b8bee8182f646baaf94598215fbf275c7fadd4ab 100644 (file)
--- a/annotate.go
+++ b/go-lightning/annotate.go
@@ -22,7 +22,7 @@ import (
        "sync"
 
        "git.arvados.org/arvados.git/sdk/go/arvados"
-       "github.com/arvados/lightning/hgvs"
+       "github.com/arvados/lightning/go-lightning/hgvs"
        log "github.com/sirupsen/logrus"
 )
 

diff --git a/arvados.go b/go-lightning/arvados.go
similarity index 100%
rename from arvados.go
rename to go-lightning/arvados.go

diff --git a/batchargs.go b/go-lightning/batchargs.go
similarity index 100%
rename from batchargs.go
rename to go-lightning/batchargs.go

diff --git a/chisquare.go b/go-lightning/chisquare.go
similarity index 100%
rename from chisquare.go
rename to go-lightning/chisquare.go

diff --git a/chisquare_test.go b/go-lightning/chisquare_test.go
similarity index 100%
rename from chisquare_test.go
rename to go-lightning/chisquare_test.go

diff --git a/choosesamples.go b/go-lightning/choosesamples.go
similarity index 100%
rename from choosesamples.go
rename to go-lightning/choosesamples.go

diff --git a/cmd.go b/go-lightning/cmd.go
similarity index 100%
rename from cmd.go
rename to go-lightning/cmd.go

diff --git a/diff.go b/go-lightning/diff.go
similarity index 97%
rename from diff.go
rename to go-lightning/diff.go
index 4999643e998e09d0fb9bf387e364c1be494acc6e..a10d6d8180d20d3150dd94c8271c89fda6c4f9d5 100644 (file)
--- a/diff.go
+++ b/go-lightning/diff.go
@@ -12,7 +12,7 @@ import (
        "io"
        "os"
 
-       "github.com/arvados/lightning/hgvs"
+       "github.com/arvados/lightning/go-lightning/hgvs"
 )
 
 type diffFasta struct{}

diff --git a/diff_test.go b/go-lightning/diff_test.go
similarity index 100%
rename from diff_test.go
rename to go-lightning/diff_test.go

diff --git a/dump.go b/go-lightning/dump.go
similarity index 100%
rename from dump.go
rename to go-lightning/dump.go

diff --git a/dumpgob.go b/go-lightning/dumpgob.go
similarity index 100%
rename from dumpgob.go
rename to go-lightning/dumpgob.go

diff --git a/export.go b/go-lightning/export.go
similarity index 99%
rename from export.go
rename to go-lightning/export.go
index 39af631e9a4e0b552f2e507f7c0fe37ffb17bed4..acb06a46e5b84b70767f59173cea0814016c58ba 100644 (file)
--- a/export.go
+++ b/go-lightning/export.go
@@ -24,7 +24,7 @@ import (
        "time"
 
        "git.arvados.org/arvados.git/sdk/go/arvados"
-       "github.com/arvados/lightning/hgvs"
+       "github.com/arvados/lightning/go-lightning/hgvs"
        "github.com/klauspost/pgzip"
        "github.com/kshedden/gonpy"
        "github.com/sirupsen/logrus"

diff --git a/export_test.go b/go-lightning/export_test.go
similarity index 100%
rename from export_test.go
rename to go-lightning/export_test.go

diff --git a/exportnumpy.go b/go-lightning/exportnumpy.go
similarity index 99%
rename from exportnumpy.go
rename to go-lightning/exportnumpy.go
index 698180b7545664ad53ce2e6002032b802fde4f5c..c0f3e55300023d0469bb718010deb5ceac169dc3 100644 (file)
--- a/exportnumpy.go
+++ b/go-lightning/exportnumpy.go
@@ -23,7 +23,7 @@ import (
        "sync/atomic"
 
        "git.arvados.org/arvados.git/sdk/go/arvados"
-       "github.com/arvados/lightning/hgvs"
+       "github.com/arvados/lightning/go-lightning/hgvs"
        "github.com/kshedden/gonpy"
        "github.com/sirupsen/logrus"
        log "github.com/sirupsen/logrus"

diff --git a/exportnumpy_test.go b/go-lightning/exportnumpy_test.go
similarity index 100%
rename from exportnumpy_test.go
rename to go-lightning/exportnumpy_test.go

diff --git a/filter.go b/go-lightning/filter.go
similarity index 100%
rename from filter.go
rename to go-lightning/filter.go

diff --git a/flake.go b/go-lightning/flake.go
similarity index 100%
rename from flake.go
rename to go-lightning/flake.go

diff --git a/glm.go b/go-lightning/glm.go
similarity index 100%
rename from glm.go
rename to go-lightning/glm.go

diff --git a/glm_test.go b/go-lightning/glm_test.go
similarity index 100%
rename from glm_test.go
rename to go-lightning/glm_test.go

diff --git a/go.mod b/go-lightning/go.mod
similarity index 97%
rename from go.mod
rename to go-lightning/go.mod
index 8f8400a3b8e351c5faf6fd92502f3463447f6b72..a38de1bee8f826970997c4d90a24146087097fd1 100644 (file)
--- a/go.mod
+++ b/go-lightning/go.mod
@@ -1,6 +1,6 @@
-module github.com/arvados/lightning
+module github.com/arvados/lightning/go-lightning
 
-go 1.17
+go 1.20
 
 require (
        git.arvados.org/arvados.git v0.0.0-20221110193247-c80603fb6b95

diff --git a/go.sum b/go-lightning/go.sum
similarity index 100%
rename from go.sum
rename to go-lightning/go.sum

diff --git a/gob.go b/go-lightning/gob.go
similarity index 100%
rename from gob.go
rename to go-lightning/gob.go

diff --git a/hgvs/diff.go b/go-lightning/hgvs/diff.go
similarity index 100%
rename from hgvs/diff.go
rename to go-lightning/hgvs/diff.go

diff --git a/hgvs/diff_test.go b/go-lightning/hgvs/diff_test.go
similarity index 100%
rename from hgvs/diff_test.go
rename to go-lightning/hgvs/diff_test.go

diff --git a/import.go b/go-lightning/import.go
similarity index 100%
rename from import.go
rename to go-lightning/import.go

diff --git a/lightning/main.go b/go-lightning/lightning/main.go
similarity index 74%
rename from lightning/main.go
rename to go-lightning/lightning/main.go
index 5d5ec6cb12314d2cc2735518f629814aa8de798b..7d4ca168e51178de895edf2dce538cc144e98806 100644 (file)
--- a/lightning/main.go
+++ b/go-lightning/lightning/main.go
@@ -4,7 +4,7 @@
 
 package main
 
-import "github.com/arvados/lightning"
+import "github.com/arvados/lightning/go-lightning"
 
 func main() {
        lightning.Main()

diff --git a/lis.go b/go-lightning/lis.go
similarity index 100%
rename from lis.go
rename to go-lightning/lis.go

diff --git a/lis_test.go b/go-lightning/lis_test.go
similarity index 100%
rename from lis_test.go
rename to go-lightning/lis_test.go

diff --git a/manhattan.go b/go-lightning/manhattan.go
similarity index 100%
rename from manhattan.go
rename to go-lightning/manhattan.go

diff --git a/manhattan.py b/go-lightning/manhattan.py
similarity index 100%
rename from manhattan.py
rename to go-lightning/manhattan.py

diff --git a/mask.go b/go-lightning/mask.go
similarity index 100%
rename from mask.go
rename to go-lightning/mask.go

diff --git a/mask_test.go b/go-lightning/mask_test.go
similarity index 100%
rename from mask_test.go
rename to go-lightning/mask_test.go

diff --git a/merge.go b/go-lightning/merge.go
similarity index 100%
rename from merge.go
rename to go-lightning/merge.go

diff --git a/numpycomvar.go b/go-lightning/numpycomvar.go
similarity index 100%
rename from numpycomvar.go
rename to go-lightning/numpycomvar.go

diff --git a/pca_plot.go b/go-lightning/pca_plot.go
similarity index 100%
rename from pca_plot.go
rename to go-lightning/pca_plot.go

diff --git a/pca_plot.py b/go-lightning/pca_plot.py
similarity index 100%
rename from pca_plot.py
rename to go-lightning/pca_plot.py

diff --git a/pipeline_test.go b/go-lightning/pipeline_test.go
similarity index 100%
rename from pipeline_test.go
rename to go-lightning/pipeline_test.go

diff --git a/profile.go b/go-lightning/profile.go
similarity index 100%
rename from profile.go
rename to go-lightning/profile.go

diff --git a/ref2genome.go b/go-lightning/ref2genome.go
similarity index 100%
rename from ref2genome.go
rename to go-lightning/ref2genome.go

diff --git a/slice.go b/go-lightning/slice.go
similarity index 100%
rename from slice.go
rename to go-lightning/slice.go

diff --git a/slice_test.go b/go-lightning/slice_test.go
similarity index 100%
rename from slice_test.go
rename to go-lightning/slice_test.go

diff --git a/slicenumpy.go b/go-lightning/slicenumpy.go
similarity index 99%
rename from slicenumpy.go
rename to go-lightning/slicenumpy.go
index 34cd777458ab93d60505b5dfa19b3aaa0280dd32..654ee6f26be7cfa9e9cf48c49268c6e469ba05d3 100644 (file)
--- a/slicenumpy.go
+++ b/go-lightning/slicenumpy.go
@@ -28,7 +28,7 @@ import (
        "unsafe"
 
        "git.arvados.org/arvados.git/sdk/go/arvados"
-       "github.com/arvados/lightning/hgvs"
+       "github.com/arvados/lightning/go-lightning/hgvs"
        "github.com/james-bowman/nlp"
        "github.com/kshedden/gonpy"
        "github.com/sirupsen/logrus"

diff --git a/stats.go b/go-lightning/stats.go
similarity index 100%
rename from stats.go
rename to go-lightning/stats.go

diff --git a/taglib.go b/go-lightning/taglib.go
similarity index 100%
rename from taglib.go
rename to go-lightning/taglib.go

diff --git a/taglib_test.go b/go-lightning/taglib_test.go
similarity index 100%
rename from taglib_test.go
rename to go-lightning/taglib_test.go

diff --git a/testdata/a.1.fasta b/go-lightning/testdata/a.1.fasta
similarity index 100%
rename from testdata/a.1.fasta
rename to go-lightning/testdata/a.1.fasta

diff --git a/testdata/a.2.fasta b/go-lightning/testdata/a.2.fasta
similarity index 100%
rename from testdata/a.2.fasta
rename to go-lightning/testdata/a.2.fasta

diff --git a/testdata/pipeline1/input1.1.fasta b/go-lightning/testdata/pipeline1/input1.1.fasta
similarity index 100%
rename from testdata/pipeline1/input1.1.fasta
rename to go-lightning/testdata/pipeline1/input1.1.fasta

diff --git a/testdata/pipeline1/input1.2.fasta b/go-lightning/testdata/pipeline1/input1.2.fasta
similarity index 100%
rename from testdata/pipeline1/input1.2.fasta
rename to go-lightning/testdata/pipeline1/input1.2.fasta

diff --git a/testdata/pipeline1/input2.1.fasta b/go-lightning/testdata/pipeline1/input2.1.fasta
similarity index 100%
rename from testdata/pipeline1/input2.1.fasta
rename to go-lightning/testdata/pipeline1/input2.1.fasta

diff --git a/testdata/pipeline1/input2.2.fasta b/go-lightning/testdata/pipeline1/input2.2.fasta
similarity index 100%
rename from testdata/pipeline1/input2.2.fasta
rename to go-lightning/testdata/pipeline1/input2.2.fasta

diff --git a/testdata/ref.fasta b/go-lightning/testdata/ref.fasta
similarity index 100%
rename from testdata/ref.fasta
rename to go-lightning/testdata/ref.fasta

diff --git a/testdata/spanningtile/input1.1.fasta b/go-lightning/testdata/spanningtile/input1.1.fasta
similarity index 100%
rename from testdata/spanningtile/input1.1.fasta
rename to go-lightning/testdata/spanningtile/input1.1.fasta

diff --git a/testdata/spanningtile/input1.2.fasta b/go-lightning/testdata/spanningtile/input1.2.fasta
similarity index 100%
rename from testdata/spanningtile/input1.2.fasta
rename to go-lightning/testdata/spanningtile/input1.2.fasta

diff --git a/testdata/spanningtile/input2.1.fasta b/go-lightning/testdata/spanningtile/input2.1.fasta
similarity index 100%
rename from testdata/spanningtile/input2.1.fasta
rename to go-lightning/testdata/spanningtile/input2.1.fasta

diff --git a/testdata/spanningtile/input2.2.fasta b/go-lightning/testdata/spanningtile/input2.2.fasta
similarity index 100%
rename from testdata/spanningtile/input2.2.fasta
rename to go-lightning/testdata/spanningtile/input2.2.fasta

diff --git a/testdata/tags b/go-lightning/testdata/tags
similarity index 100%
rename from testdata/tags
rename to go-lightning/testdata/tags

diff --git a/testdata/tinyref.fasta b/go-lightning/testdata/tinyref.fasta
similarity index 100%
rename from testdata/tinyref.fasta
rename to go-lightning/testdata/tinyref.fasta

diff --git a/throttle.go b/go-lightning/throttle.go
similarity index 100%
rename from throttle.go
rename to go-lightning/throttle.go

diff --git a/tilelib.go b/go-lightning/tilelib.go
similarity index 100%
rename from tilelib.go
rename to go-lightning/tilelib.go

diff --git a/tilelib_test.go b/go-lightning/tilelib_test.go
similarity index 100%
rename from tilelib_test.go
rename to go-lightning/tilelib_test.go

diff --git a/tilestats.go b/go-lightning/tilestats.go
similarity index 100%
rename from tilestats.go
rename to go-lightning/tilestats.go

diff --git a/vcf2fasta.go b/go-lightning/vcf2fasta.go
similarity index 100%
rename from vcf2fasta.go
rename to go-lightning/vcf2fasta.go

diff --git a/version.sh b/go-lightning/version.sh
similarity index 100%
rename from version.sh
rename to go-lightning/version.sh