view env/lib/python3.9/site-packages/galaxy/tool_util/deps/mulled/invfile.lua @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

-- http://stackoverflow.com/questions/19262761/lua-need-to-split-at-comma/19263313#19263313
function string:split( inSplitPattern, outResults )
  if not outResults then
    outResults = { }
  end
  local theStart = 1
  local theSplitStart, theSplitEnd = string.find( self, inSplitPattern, theStart )
  while theSplitStart do
    table.insert( outResults, string.sub( self, theStart, theSplitStart-1 ) )
    theStart = theSplitEnd + 1
    theSplitStart, theSplitEnd = string.find( self, inSplitPattern, theStart )
  end
  table.insert( outResults, string.sub( self, theStart ) )
  return outResults
end

local repo = VAR.REPO

local channel_args = ''
local channels = VAR.CHANNELS:split(",")
for i = 1, #channels do
    channel_args = channel_args .. " -c '" .. channels[i] .. "'"
end

local target_args = ''
local targets = VAR.TARGETS:split(",")
for i = 1, #targets do
    target_args = target_args .. " '" .. targets[i] .. "'"
end

local bind_args = {}
local binds_table = VAR.BINDS:split(",")
for i = 1, #binds_table do
    table.insert(bind_args, binds_table[i])
end

local test_bind_args = {}
local test_binds_table = VAR.TEST_BINDS:split(",")
for i = 1, #test_binds_table do
    table.insert(test_bind_args, test_binds_table[i])
end

local conda_image = VAR.CONDA_IMAGE
if conda_image == '' then
    conda_image = 'continuumio/miniconda3:latest'
end


local singularity_image = VAR.SINGULARITY_IMAGE
if singularity_image == '' then
    singularity_image = 'quay.io/biocontainers/singularity:2.4.6--0'
end

local singularity_image_dir = VAR.SINGULARITY_IMAGE_DIR
if singularity_image_dir == '' then
    singularity_image_dir = 'singularity_import'
end



local destination_base_image = VAR.DEST_BASE_IMAGE
if destination_base_image == '' then
    destination_base_image = 'bgruening/busybox-bash:0.1'
end

local verbose = VAR.VERBOSE
if verbose == '' then
    verbose = '--quiet'
else
    verbose = '--verbose'
end

local preinstall = VAR.PREINSTALL
if preinstall ~= '' then
    preinstall = preinstall .. ' && '
end

local postinstall = VAR.POSTINSTALL
if postinstall ~= '' then
    postinstall = '&&' .. postinstall
end

inv.task('build')
    .using(conda_image)
        .withHostConfig({binds = {"build:/data"}})
        .run('rm', '-rf', '/data/dist')
    .using(conda_image)
        .withHostConfig({binds = bind_args})
        .run('/bin/sh', '-c', preinstall
            .. 'conda install '
            .. channel_args .. ' '
            .. target_args
            .. ' -p /usr/local --copy --yes '
            .. verbose
            .. postinstall)
    .wrap('build/dist')
        .at('/usr/local')
        .inImage(destination_base_image)
        .as(repo)

if VAR.SINGULARITY ~= '' then
    inv.task('singularity')
        .using(singularity_image)
        .withHostConfig({binds = {"build:/data", "'" .. singularity_image_dir .. "':/import"}, privileged = true})
        .withConfig({entrypoint = {'/bin/sh', '-c'}})
        .run('mkdir', '-p', '/usr/local/var/singularity/mnt/container')
        .run('singularity', 'build', '/import/' .. VAR.SINGULARITY_IMAGE_NAME, '/import/Singularity.def')
        .run('chown', VAR.USER_ID, '/import/' .. VAR.SINGULARITY_IMAGE_NAME)
end

inv.task('cleanup')
    .using(conda_image)
    .withHostConfig({binds = {"build:/data"}})
    .run('rm', '-rf', '/data/dist')


if VAR.TEST_BINDS == '' then
    inv.task('test')
        .using(repo)
        .withConfig({entrypoint = {'/bin/sh', '-c'}})
        .run(VAR.TEST)
else
    inv.task('test')
        .using(repo)
        .withHostConfig({binds = test_bind_args})
        .withConfig({entrypoint = {'/bin/sh', '-c'}})
        .run(VAR.TEST)
end

inv.task('push')
    .push(repo)

inv.task('build-and-test')
    .runTask('build')
    .runTask('singularity')
    .runTask('cleanup')
    .runTask('test')


inv.task('all')
    .runTask('build')
    .runTask('singularity')
    .runTask('cleanup')
    .runTask('test')
    .runTask('push')