Commit f29814e5 authored by Koehorst, Jasper's avatar Koehorst, Jasper
Browse files

upload added

parent 3f15d7b6
Pipeline #17958 failed with stage
in 1 minute and 10 seconds
......@@ -14,8 +14,9 @@ test_build_dev:
stage: test_build
script:
- ./build.sh
- FILENAME=./iRODSKubernetes.jar
- /upload.sh $FILENAME
- curl --insecure --user $USERNAME:$PASSWORD -T ./iRODSKubernetes.jar sftp://download.systemsbiology.nl/unlock/
# - FILENAME=./iRODSKubernetes.jar
# - /upload.sh $FILENAME
only:
- dev
......@@ -24,7 +25,8 @@ test_build_master:
stage: test_build
script:
- ./build.sh
- FILENAME=./iRODSKubernetes.jar
- /upload.sh $FILENAME
- curl --insecure --user $USERNAME:$PASSWORD -T ./iRODSKubernetes.jar sftp://download.systemsbiology.nl/unlock/
# - FILENAME=./iRODSKubernetes.jar
# - /upload.sh $FILENAME
only:
- master
package nl.munlock.objects;
import nl.munlock.Generic;
import nl.munlock.yaml.MetaGenomics;
import nl.munlock.yaml.Yaml;
import org.apache.log4j.Logger;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
public class WorkflowMetagenomics extends Workflow {
private static final Logger log = Generic.getLogger(WorkflowMetagenomics.class, Yaml.debug);
public String destination;
public HashMap<String, String> irods = new HashMap<>();
public ArrayList<FileClass> forward_reads = new ArrayList<>();
public ArrayList<FileClass> reverse_reads = new ArrayList<>();
public ArrayList<FileClass> pacbio_reads = new ArrayList<>();
public String kraken_database; // = new ArrayList<>();
public boolean isolate;
public boolean metagenomics;
public Map<String, String> clazz;
public void addIRODS(String irodsPath) {
irods.put(irods.size() + "_irods", irodsPath);
}
public void setDestination(String destination) {
this.destination = destination;
}
public String getDestination() {
return destination;
}
public ArrayList<FileClass> getForward_reads() {
return forward_reads;
}
public void addForward_reads(String forward_reads) throws Exception {
addIRODS(forward_reads);
FileClass fileClass = new FileClass();
fileClass.setClazz("File");
fileClass.setLocation(forward_reads);
this.forward_reads.add(fileClass);
}
public boolean isIsolate() {
return isolate;
}
public void setIsolate(boolean isolate) {
this.isolate = isolate;
}
public ArrayList<FileClass> getReverse_reads() {
return reverse_reads;
}
public void addReverse_reads(String reverse_reads) throws Exception {
addIRODS(reverse_reads);
FileClass fileClass = new FileClass();
fileClass.setClazz("File");
fileClass.setLocation(reverse_reads);
this.reverse_reads.add(fileClass);
}
public ArrayList<FileClass> getPacbio() {
return pacbio_reads;
}
public void addPacbio(String pacbio) throws Exception {
addIRODS(pacbio);
FileClass fileClass = new FileClass();
fileClass.setClazz("File");
fileClass.setLocation(pacbio);
this.pacbio_reads.add(fileClass);
}
public boolean isMetagenomics() {
return metagenomics;
}
public void setMetagenomics(boolean metagenomics) {
this.metagenomics = metagenomics;
}
public String getKraken_database() {
return kraken_database;
}
public void setKraken_database(String kraken_database) throws Exception {
this.kraken_database = kraken_database;
// FileClass fileClass = new FileClass();
// fileClass.setClazz("Directory");
// fileClass.setLocation(kraken_database);
// this.kraken_database.add(fileClass);
}
}
package nl.munlock.options.workflow;
import com.beust.jcommander.JCommander;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.ParameterException;
import java.lang.reflect.Field;
public class CommandOptionsNGTAX extends CommandOptionsYAML {
@Parameter(names = {"-length"}, description = "Read length used in NGTAX (default maximum length)")
public int read_len = 0;
@Parameter(names = {"-minimumThreshold"}, description = "Minimum threshold detectable, expressed in percentage")
public double minimumThreshold = 0.1;
@Parameter(names = {"-referenceDB"}, description = "Reference database to disable provide empty string -referenceDB ''")
public String reference_db = "/unlock/references/databases/Silva/SILVA_132_SSURef_tax_silva.fasta.gz";
public CommandOptionsNGTAX(String args[]) {
try {
JCommander jc = new JCommander(this);
jc.parse(args);
// if any of the nl.wur.ssb.options is null...
boolean failed = false;
for (Field f : getClass().getDeclaredFields())
if (f.get(this) == null) {
System.err.println(f + " system variable not found, see help for more information");
failed = true;
}
if (this.help || failed) {
throw new ParameterException("something failed");
}
} catch (ParameterException | IllegalAccessException pe) {
int exitCode = 64;
if (this.help) {
exitCode = 0;
}
System.out.println(pe.getMessage());
new JCommander(this).usage();
System.out.println(" * required parameter");
System.exit(exitCode);
}
}
}
package nl.munlock.yaml;public class HDT {
}
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