pvanheus

__default__:
    nCPUs     : 1
    memory    : 10000
    name      : "mykrobe.{rule}.{wildcards}"
    output    : "logs/cluster_{rule}.{wildcards}.o"
    error     : "logs/cluster_{rule}.{wildcards}.e"


map_minimap2:
    nCPUs     : 16

pvanheus

class: CommandLineTool
cwlVersion: v1.0
$namespaces:
  s: 'http://schema.org/'
baseCommand:
  - porechop
inputs:
  output_format:
    type:
      - 'null'

pvanheus

study_accession	sample_accession	secondary_sample_accession	experiment_accession	run_accession	tax_id	scientific_name	instrument_model	library_layout	fastq_ftp	fastq_galaxy	submitted_ftp	submitted_galaxy	sra_ftp	sra_galaxy	cram_index_ftp	cram_index_galaxy
PRJEB22237	SAMEA104221057	ERS1880075	ERX2157080	ERR2099775	1773	Mycobacterium tuberculosis	Illumina MiSeq	PAIRED	ftp.sra.ebi.ac.uk/vol1/fastq/ERR209/005/ERR2099775/ERR2099775_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR209/005/ERR2099775/ERR2099775_2.fastq.gz	ftp.sra.ebi.ac.uk/vol1/fastq/ERR209/005/ERR2099775/ERR2099775_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR209/005/ERR2099775/ERR2099775_2.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR209/ERR2099775/G1003mi_G249_1.filtered.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR209/ERR2099775/G1003mi_G249_2.filtered.fastq.gz	ftp.sra.ebi.ac.uk/vol1/run/ERR209/ERR2099775/G1003mi_G249_1.filtered.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR209/ERR2099775/G1003mi_G249_2.filtered.fastq.gz	ftp.sra.ebi.ac.uk/vol1/err/ERR209/005/ERR2099775	ft

pvanheus

vl = QgsVectorLayer("Point?crs=epsg:4326&field=id:integer&field=name:string(20)&index=yes", "temporary_points", "memory")
pr = vl.dataProvider()
pr.addAttributes([QgsField("name", QVariant.String), QgsField("age",  QVariant.Int), QgsField("size", QVariant.Double)])
vl.updateFields()

fet = QgsFeature()
fet.setGeometry(QgsGeometry.fromPointXY(QgsPointXY(10,10)))
fet.setAttributes(["Johny", 2, 0.3])
pr.addFeatures([fet])

pvanheus

{"failed": true, "dataset_id": 68, "type": "dataset", "ext": "data", "stderr": "Failed to find file_path %s.bkp in {u'%s.idx': {u'name': u'hard_masked_seabass_genome.seq', u'file_type': u'spalndbnp', u'space_to_tab': False, u'uuid': None, u'dbkey': u'?', u'auto_decompress': True, u'path': u'/home/pvh/Documents/code/Masters/galaxy/database/tmp/upload_file_data_xU_6zT', u'purge_source': True, u'type': u'file', u'to_posix_lines': True}, u'%s.seq': {u'name': u'hard_masked_seabass_genome.bkn', u'file_type': u'spalndbnp', u'space_to_tab': False, u'uuid': None, u'dbkey': u'?', u'auto_decompress': True, u'path': u'/home/pvh/Documents/code/Masters/galaxy/database/tmp/upload_file_data_qpUHCf', u'purge_source': True, u'type': u'file', u'to_posix_lines': True}, u'%s.bkn': {u'name': u'hard_masked_seabass_genome.bkp', u'file_type': u'spalndbnp', u'space_to_tab': False, u'uuid': None, u'dbkey': u'?', u'auto_decompress': True, u'path': u'/home/pvh/Documents/code/Masters/galaxy/database/tmp/upload_file_data_p1w3_I', u'purge_s

pvanheus

cd client && yarn run build
yarn run v1.15.2
$ NODE_ENV=development gulp staging && concurrently -r "yarn run webpack" "yarn run gulp clean && yarn run gulp" && yarn run save-build-hash
[15:27:36] Using gulpfile /tools/software/galaxy/galaxy1/client/gulpfile.js
[15:27:36] Starting 'stage-libs'...
[15:27:36] Starting 'fonts'...
[15:27:36] Finished 'fonts' after 511 ms
$ gulp clean
$ webpack -d
[15:28:09] Using gulpfile /tools/software/galaxy/galaxy1/client/gulpfile.js

pvanheus

No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for dtoolcore
INFO:conda_build.metadata:Attempting to finalize metadata for dtoolcore
Traceback (most recent call last):
  File "/usr/people/pvh/miniconda3/lib/python3.6/site-packages/urllib3/contrib/pyopenssl.py", line 280, in recv_into
    return self.connection.recv_into(*args, **kwargs)
  File "/usr/people/pvh/miniconda3/lib/python3.6/site-packages/OpenSSL/SSL.py", line 1814, in recv_into

pvanheus

dna = 'ctgtaacttagttggctctttcgtagcccattgtcgggctagctatttcactcccgcgggggtctccgcgtggatggt'
codon1 = dna[0:3]
codon2 = dna[3:6]
codon3 = dna[6:9]
codon4 = dna[12:15]
codon5 = dna[15:18]
print(codon1)
print(codon2)
print(codon3)
print(codon4)

pvanheus

pattern_buffer[pattern_counter] = c;
output_buffer.write(&pattern_buffer[0..pattern_counter+1]).expect("failed to write pattern buffer to output file");
state = 4;
pattern_counter = 0;

pvanheus

Mycobacterium avium subsp. paratuberculosis K-10 GCF_000007865.1
Mycobacterium avium 104 GCF_000014985.1
Mycobacterium avium subsp. paratuberculosis MAP4 GCF_000390085.1
Mycobacterium avium subsp. avium 2285 (R) GCF_000758285.1
Mycobacterium avium subsp. avium GCF_000770235.1
Mycobacterium avium subsp. hominissuis TH135 GCF_000829075.1
Mycobacterium avium subsp. avium 2285 (S) GCF_000831285.1
Mycobacterium avium subsp. paratuberculosis GCF_000835225.1
Mycobacterium avium subsp. paratuberculosis GCF_000835265.1
Mycobacterium avium subsp. paratuberculosis GCF_001653355.1