Commit dd02aeaa authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

download job file instead of network mount

parent dfd4144d
......@@ -29,8 +29,10 @@ public class App {
// Make the irods connection
Connection connection = new Connection(commandOptions);
// Downloading job files
Scanner scanner = new Scanner(new File(commandOptions.jobFile));
// Downloading job file
nl.munlock.irods.Generic.downloadFile(connection, new File(commandOptions.jobFile));
Scanner scanner = new Scanner(new File("." + commandOptions.jobFile));
HashSet<String> hdts = new HashSet<>();
HashSet<String> turtles = new HashSet<>();
ArrayList<String> lines = new ArrayList<>();
......
......@@ -11,10 +11,10 @@ public class AppTest {
@Test
public void testPhyloseq() throws Exception {
String[] args = {
"-i", "/Volumes/unlock-icat.irods.surfsara.nl/home/koehorst/phyloseq/MIB-Amplicon.job",
"-i", "/unlock/home/koehorst/phyloseq/TKI_BO3B.job",
"-database", "SILVA_138.1_SSURef_tax_silva.fasta.gz",
"-readLength", "70",
"-prefix", "MIB-AmpliconX"
"-readLength", "100",
"-prefix", "TKI_BO3B"
};
App.main(args);
}
......
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