internal static WSLProxyResponse VFabricate()
{
// ./VFabricateBioSeqDB.sh ${samplepath} $contig $vfabricate $output path
//# $1 Sample name (Use 'Abricate' when no sample picked).
//# $2 Input contig path
//# $3 Gene XRef path
//# $4 Output folder
string inputFile = AppConfigHelper.NormalizePathToLinux(AppConfigHelper.InputPath("VFabricate"));
string sampleName = "Abricate";
if (AppConfigHelper.SampleChecked("VFabricate"))
{
// First extract the fasta file from the database.
sampleName = AppConfigHelper.SampleID("VFabricate");
WSLProxyResponse WSLResponse = ExtractSample(sampleName, AppConfigHelper.NormalizePathToLinux("C:\\Temp"));
if (WSLResponse.ExitCode != 0)
{
return(WSLResponse);
}
inputFile = AppConfigHelper.NormalizePathToLinux("C:\\Temp") + "/" + AppConfigHelper.SampleID("VFabricate") + ".fasta";
}
AppConfigHelper.LastCommand = AppConfigHelper.CondaPrefixAbricate() + " ~/VFabricateBioSeqDB.sh " + sampleName + " " + inputFile + " " +
AppConfigHelper.NormalizePathToLinux(AppConfigHelper.VFabricateGeneXref) + " " +
AppConfigHelper.NormalizePathToLinux(AppConfigHelper.OutputPath("VFabricate")
//+ " &> /mnt/c/Temp/stderr.txt"
);
return(StandardCallToWSL());
}
internal static WSLProxyResponse Quast()
{
// /usr/local/quast-5.0.2/quast.py -o quastRA --glimmer $contig
string inputFile = AppConfigHelper.NormalizePathToLinux(AppConfigHelper.InputPath("Quast"));
string sampleName = "Quast";
if (AppConfigHelper.SampleChecked("Quast"))
{
// First extract the fasta file from the database.
sampleName = AppConfigHelper.SampleID("Quast");
WSLProxyResponse WSLResponse = ExtractSample(sampleName, AppConfigHelper.NormalizePathToLinux("C:\\Temp"));
if (WSLResponse.ExitCode != 0)
{
return(WSLResponse);
}
inputFile = AppConfigHelper.NormalizePathToLinux("C:\\Temp") + "/" + AppConfigHelper.SampleID("Quast") + ".fasta";
}
AppConfigHelper.LastCommand = "/usr/local/quast-5.0.2/quast.py -o " + AppConfigHelper.NormalizePathToLinux(AppConfigHelper.OutputPath("Quast") +
"/quast" + sampleName + " --glimmer " + inputFile
//+ " &> /mnt/c/Temp/stderr.txt"
);
return(StandardCallToWSL());
}
private void mnuRemove_Click(object sender, EventArgs e)
{
BioSeqRemove frm = new BioSeqRemove();
DialogResult rc = frm.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs
{
Cursor.Current = Cursors.WaitCursor;
//int ret = SeqDBHelper.RemoveSample(); // Parameters are in appsettings.
WSLProxyResponse WSLResponse = ServiceCallHelper.RemoveSample(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
MessageBox.Show(AppConfigHelper.RemoveSampleID() + " successfully removed.", "Success", MessageBoxButtons.OK);
AppConfigHelper.RemoveSample(string.Empty); // So we don't prompt for it again.
ReloadSampleIDs(); // Reload list without sample ID.
}
else
{
MessageBox.Show("Remove completed with error code " + WSLResponse.ExitCode.ToString() + "." + Environment.NewLine + Environment.NewLine +
AppConfigHelper.StandardOutput + Environment.NewLine + AppConfigHelper.LastError, "Error", MessageBoxButtons.OK);
}
}
}
private void backgroundWorker_DoWork(object sender, System.ComponentModel.DoWorkEventArgs e)
{
BioSeqTask task = AppConfigHelper.TaskOfID(AppConfigHelper.LastTaskID);
WSLProxyResponse WSLResponse = null;
switch (task.TaskType)
{
case "Centrifuge":
WSLResponse = ServiceCallHelper.Centrifuge(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Salmonella":
WSLResponse = ServiceCallHelper.Salmonella(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "VFabricate":
WSLResponse = ServiceCallHelper.VFabricate(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Search":
WSLResponse = ServiceCallHelper.SearchSample(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Kraken2":
WSLResponse = ServiceCallHelper.Kraken2(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Quast":
WSLResponse = ServiceCallHelper.Quast(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "BBMap":
WSLResponse = ServiceCallHelper.BBMap(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "BuildTree":
WSLResponse = ServiceCallHelper.BuildTree(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Assemble":
WSLResponse = ServiceCallHelper.Assemble(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig(), AppConfigHelper.QuerySampleConfig());
break;
case "InfluenzaA":
WSLResponse = ServiceCallHelper.InfluenzaA(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
case "Nextstrain":
WSLResponse = ServiceCallHelper.Nextstrain(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
break;
}
task.LastError = WSLResponse.StandardError;
task.StandardOutput = WSLResponse.StandardOutput;
e.Result = new List <object>()
{
WSLResponse.ExitCode, task
};
}
private void btnReset_Click(object sender, EventArgs e)
{
Cursor.Current = Cursors.WaitCursor;
WSLProxyResponse WSLResponse = BioSeqDBModel.Instance.NextstrainReset(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig());
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
MessageBox.Show("Nextstrain reset complete.", "COMPLETE", MessageBoxButtons.OK);
}
else
{
MessageBox.Show("Nextstrain reset error " + WSLResponse.ExitCode.ToString() + Environment.NewLine +
WSLResponse.StandardError + ".", "ERROR", MessageBoxButtons.OK);
}
}
public static WSLProxyResponse Kraken2()
{
WSLProxyResponse WSLResponse = null;
string inputFile = AppConfigHelper.NormalizePathToLinux(AppConfigHelper.InputPath("Kraken2"));
if (AppConfigHelper.SampleChecked("Kraken2"))
{
// First extract the fasta file from the database.
WSLResponse = ExtractSample(AppConfigHelper.SampleID("Kraken2"), AppConfigHelper.NormalizePathToLinux("C:\\Temp"));
if (WSLResponse.ExitCode == 0)
{
inputFile = AppConfigHelper.NormalizePathToLinux("C:\\Temp") + "/" + AppConfigHelper.SampleID("Kraken2") + ".fasta";
}
else
{
return(WSLResponse);
}
}
// eg. /usr/local/kraken2/kraken2 --db /data/referenceDB/minikraken2_v1_8GB/ --threads 64 --report kraken.aggregates.txt --use-names --output kraken.txt $contig
// conda run -n refseq_masher-0.1.1 refseq_masher matches --output-type tab -o RefseqIdent.txt $contig
AppConfigHelper.LastCommand = "/usr/local/kraken2/kraken2 --db /data/referenceDB/minikraken2_v1_8GB/ --threads 16 --report " +
AppConfigHelper.NormalizePathToLinux(AppConfigHelper.OutputPath("Kraken2") + "/kraken.aggregates.txt") + " --use-names --output " +
AppConfigHelper.NormalizePathToLinux(AppConfigHelper.OutputPath("Kraken2") + "/kraken.txt") + " " + inputFile;
WSLResponse = StandardCallToWSL();
if (WSLResponse.ExitCode == 0)
{
AppConfigHelper.LastCommand = "conda run -n refseq_masher-0.1.1 refseq_masher matches --output-type tab -o " +
AppConfigHelper.NormalizePathToLinux(AppConfigHelper.OutputPath("Kraken2") + "/RefseqIdent.txt ") + inputFile;
if (AppConfigHelper.SampleChecked("Kraken2"))
{
File.Delete("C:\\Temp\\" + AppConfigHelper.SampleID("Kraken2") + ".fasta");
}
return(StandardCallToWSL());
}
return(WSLResponse);
}
private void mnuRestore_Click(object sender, EventArgs e)
{
BioSeqRestore frm = new BioSeqRestore(txtVersions.Text.Trim());
DialogResult rc = frm.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs
{
Cursor.Current = Cursors.WaitCursor;
WSLProxyResponse WSLResponse = ServiceCallHelper.RestoreDatabase(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
ReloadSampleIDs(); // Reload list without sample ID.
MessageBox.Show(AppConfigHelper.StandardOutput + Environment.NewLine + "Restore successfully completed.", "Success", MessageBoxButtons.OK);
}
else
{
MessageBox.Show("Restore completed with error code " + WSLResponse.ExitCode.ToString() + "." + Environment.NewLine + Environment.NewLine +
AppConfigHelper.StandardOutput + Environment.NewLine + AppConfigHelper.LastError, "Error", MessageBoxButtons.OK);
}
}
}
private static WSLProxyResponse StandardCallToWSL()
{
//string prefix = "cd;export PATH=/home/arnie/.local/bin:/home/arnie/bin:/snap/bin:/home/arnie/.dotnet/tools:$PATH;"; // Prepend to each invocation of wsl.
AppConfigHelper.StandardOutput = string.Empty;
AppConfigHelper.LastError = string.Empty;
AppConfigHelper.LastExitCode = 0;
Logger.Log.Debug("StandardCallToWSL: " + AppConfigHelper.LastUser + " CMD: " + AppConfigHelper.LastCommand);
var info = new ProcessStartInfo(AppConfigHelper.PathToWSL(), "bash -ic '" + AppConfigHelper.CondaPrefix() + " " + AppConfigHelper.LastCommand + "'")
{
WorkingDirectory = AppConfigHelper.NormalizePathToWindows(AppConfigHelper.LinuxHomeDirectory),
UseShellExecute = false,
CreateNoWindow = true,
RedirectStandardInput = true,
RedirectStandardOutput = true,
RedirectStandardError = true
};
WSLProxyResponse WSLResponse = new WSLProxyResponse();
int rc = -1;
using (var p = Process.Start(info))
{
p.WaitForExit();
RecordStandardOutput(p);
rc = p.ExitCode;
WSLResponse.ExitCode = rc;
WSLResponse.StandardOutput = p.StandardOutput.ReadToEnd();
WSLResponse.StandardError = p.StandardError.ReadToEnd();
p.Close();
}
return(WSLResponse);
}
private void mnuBackup_Click(object sender, EventArgs e)
{
BioSeqBackup frm = new BioSeqBackup();
DialogResult rc = frm.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs
{
Cursor.Current = Cursors.WaitCursor;
WSLProxyResponse WSLResponse = ServiceCallHelper.BackupDatabase(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
RefreshVersionInformation(AppConfigHelper.seqdbConfig.seqDBs[AppConfigHelper.seqdbConfig.LastDBSelected]);
MessageBox.Show(AppConfigHelper.StandardOutput + Environment.NewLine + "Backup successfully completed.", "Success", MessageBoxButtons.OK);
// Refresh backup version display.
}
else
{
MessageBox.Show("Backup completed with error code " + WSLResponse.ExitCode.ToString() + "." + Environment.NewLine + Environment.NewLine +
AppConfigHelper.StandardOutput + Environment.NewLine + AppConfigHelper.LastError, "Error", MessageBoxButtons.OK);
}
}
}
private void mnuExtract_Click(object sender, EventArgs e)
{
BioSeqExtract frm = new BioSeqExtract();
DialogResult rc = frm.ShowDialog();
if (rc == DialogResult.OK) // then the config has the specs
{
Cursor.Current = Cursors.WaitCursor;
// Parameters are in appsettings.
WSLProxyResponse WSLResponse = ServiceCallHelper.Extract(AppConfigHelper.LoggedOnUser, AppConfigHelper.JsonConfig()); // Parameters are in appsettings.
ServiceCallHelper.LoadConfig(AppConfigHelper.LoggedOnUser); // To retrieve StandardOutput and LastError.
Cursor.Current = Cursors.Default;
if (WSLResponse.ExitCode == 0)
{
MessageBox.Show(AppConfigHelper.StandardOutput + Environment.NewLine + "Extract completed successfully. Result is in " +
AppConfigHelper.ExtractOutputPath() + "\\" + AppConfigHelper.ExtractSampleID() + ".fasta", "Success", MessageBoxButtons.OK);
}
else
{
MessageBox.Show("Extract completed with error code " + WSLResponse.ExitCode.ToString() + "." + Environment.NewLine + Environment.NewLine +
AppConfigHelper.StandardOutput + Environment.NewLine + AppConfigHelper.LastError, "Error", MessageBoxButtons.OK);
}
}
}
internal static WSLProxyResponse BBMap()
{
WSLProxyResponse WSLResponse = null;
string inputFile = AppConfigHelper.NormalizePathToLinux(AppConfigHelper.InputPath("BBMap"));
if (AppConfigHelper.SampleChecked("BBMap"))
{
// First extract the fasta file from the database.
WSLResponse = ExtractSample(AppConfigHelper.SampleID("BBMap"), AppConfigHelper.NormalizePathToLinux("C:\\Temp"));
if (WSLResponse.ExitCode != 0)
{
return(WSLResponse);
}
inputFile = AppConfigHelper.NormalizePathToLinux("C:\\Temp") + "/" + AppConfigHelper.SampleID("BBMap") + ".fasta";
}
// Might need to consolidate multiple fastq files into one.
string fastqPath = AppConfigHelper.BBMapFastqPath();
string[] files = Directory.GetFiles(fastqPath, "*.fastq", SearchOption.TopDirectoryOnly);
if (files.Length == 0)
{
WSLResponse = new WSLProxyResponse();
WSLResponse.ExitCode = -3;
WSLResponse.StandardError = "No *.fastq files found in " + fastqPath + ".";
return(WSLResponse);
}
// cat $samplePath/*.fastq > ${sampleName}.fastq
string fastqOutput = AppConfigHelper.NormalizePathToLinux("C:\\Temp") + "/sample.fastq";
ProcessStartInfo infoCat = new ProcessStartInfo(AppConfigHelper.PathToWSL(), "bash -ic 'cat " +
AppConfigHelper.NormalizePathToLinux(fastqPath) + "/*.fastq > " + fastqOutput + "'")
{
UseShellExecute = false,
CreateNoWindow = true,
RedirectStandardInput = true,
RedirectStandardOutput = true, // We can catch the output here.
RedirectStandardError = true
};
Process P = Process.Start(infoCat);
P.WaitForExit();
int result = P.ExitCode;
if (result != 0)
{
WSLResponse = new WSLProxyResponse();
WSLResponse.ExitCode = -2;
WSLResponse.StandardError = "Catenate to output " + fastqOutput + " failed for " + fastqPath + ".";
return(WSLResponse);
}
// Convert fastq to fastq
// seqtk seq -A BC87_reads.fastq > sample.fasta
string fastaReads = AppConfigHelper.NormalizePathToLinux("C:\\Temp") + "/sample.fasta";
infoCat = new ProcessStartInfo(AppConfigHelper.PathToWSL(), "bash -ic 'seqtk seq -A " + fastqOutput + " > " + fastaReads + "'")
{
UseShellExecute = false,
CreateNoWindow = true,
RedirectStandardInput = true,
RedirectStandardOutput = true, // We can catch the output here.
RedirectStandardError = true
};
P = Process.Start(infoCat);
P.WaitForExit();
result = P.ExitCode;
if (result != 0)
{
WSLResponse = new WSLProxyResponse();
WSLResponse.ExitCode = -4;
WSLResponse.StandardError = P.StandardError.ReadToEnd();
WSLResponse.StandardOutput = P.StandardOutput.ReadToEnd();
return(WSLResponse);
}
P.Close();
// /usr/local/bbmap/bbmap.sh nodisk=f ref=BC87_trinity_assembly_minimap2/Trinity.fasta in=sample.fasta covstats=covstats.txt covhist=covhist.txt basecov=basecov.txt bincov=bincov.txt
// rm sample.fasta
string outputPath = AppConfigHelper.NormalizePathToLinux(AppConfigHelper.OutputPath("BBMap"));
string bbmapInvocation = AppConfigHelper.CondaPrefix() + " bbmap.sh"; // On my machine, bbmap.sh is installed in conda.
if (true)
{
bbmapInvocation = "/usr/local/bbmap/bbmap.sh"; // Where bbmap.sh is installed on WIMMER (set condition to true).
}
AppConfigHelper.LastCommand = bbmapInvocation + " nodisk=f ref=" + inputFile + " in=" + fastaReads + " covstats=" + outputPath +
"/covstats.txt covhist=" + outputPath + "/covhist.txt basecov=" + outputPath + "/basecov.txt bincov=" + outputPath + "/bincov.txt";
WSLResponse = StandardCallToWSL();
if (WSLResponse.ExitCode == 0)
{
AppConfigHelper.LastCommand = "conda run -n refseq_masher-0.1.1 refseq_masher matches --output-type tab -o " + outputPath + "/RefseqIdent.txt " + inputFile;
WSLResponse = StandardCallToWSL();
if (WSLResponse.ExitCode == 0)
{
if (AppConfigHelper.SampleChecked("BBMap"))
{
File.Delete("C:\\Temp\\" + AppConfigHelper.SampleID("BBMap") + ".fasta");
}
// Get rid of sample.fasta and the fastq file.
if (File.Exists(@"c:\Temp\sample.fastq"))
{
File.Delete(@"c:\Temp\sample.fastq");
}
if (File.Exists(@"c:\Temp\sample.fasta"))
{
File.Delete(@"c:\Temp\sample.fasta");
}
}
}
return(WSLResponse);
}
public static WSLProxyResponse AssembleSamples(string config)
{
// eg. ./assembleRANF.sh --fast_polish --flye –-bbmap skip|normal –-quast skip|normal –-kraken skip|normal --complete_signal /mnt/c/Temp/assemble000003.txt /mnt/c/Temp/samples.txt
File.WriteAllText("C:\\Temp\\samples.txt", config);
AppConfigHelper.StandardOutput = string.Empty;
AppConfigHelper.LastError = string.Empty;
AppConfigHelper.LastExitCode = 0;
//int taskid = AppConfigHelper.MaxTaskID() + 1;
//BioSeqTask task = new BioSeqTask()
//{
// //TaskData = @"C:\Temp\Assemble" + taskid.ToString("000000") + ".txt",
// TaskDB = string.Empty, // No database involved in context of this call.
// TaskID = taskid.ToString(),
// TaskStatus = "Pending",
// TaskTime = DateTime.Now,
// TaskComplete = DateTime.MinValue,
// TaskType = "Assemble",
// TaskUser = AppConfigHelper.LastUser,
// StandardOutput = string.Empty,
// LastError = string.Empty,
// LastExitCode = -999
//};
//AppConfigHelper.AddTask(task);
// Return contents of the TaskData file:
// Line 1: return code
// Line 2-n: standard output plus error output.
if (AppConfigHelper.AssembleTrinity())
{
string hostref = AppConfigHelper.NormalizePathToLinux(AppConfigHelper.AssembleHostReference);
AppConfigHelper.LastCommand = AppConfigHelper.PathToNextFlowScript() + " --Trinity --virusRef " +
AppConfigHelper.NormalizePathToLinux(AppConfigHelper.AssembleVirusReference) + " " +
(hostref.Length > 0 ? " --hostRef " + hostref : string.Empty) + " " + AppConfigHelper.LinuxCDrive() + "/Temp/samples.txt";
}
else
{
string VFabricate = " --VFabricate ";
if (AppConfigHelper.AssembleVFabricate())
{
VFabricate += AppConfigHelper.NormalizePathToLinux(AppConfigHelper.AssembleVFGeneXRef);
}
else
{
VFabricate += "skip";
}
AppConfigHelper.LastCommand = AppConfigHelper.PathToNextFlowScript() + " " + (AppConfigHelper.AssembleFastPolish() ? "--fast_polish" : string.Empty) + " " +
(AppConfigHelper.AssembleFlye() ? "--flye" : string.Empty) + " --bbmap " +
(AppConfigHelper.AssembleBBmap() ? "normal" : "skip") + " --quast " +
(AppConfigHelper.AssembleQuast() ? "normal" : "skip") + VFabricate + " --kraken " +
(AppConfigHelper.AssembleKraken2() ? "normal" : "skip") + " " +
AppConfigHelper.LinuxCDrive() + "/Temp/samples.txt";
}
// DEBUG HELPER:
//AppConfigHelper.LastCommand = "~/makeassemble.sh " + AppConfigHelper.NormalizePathToLinux(task.TaskData);
//AppConfigHelper.LastCommand = "~/assembleRA.sh PDS2021318subset /mnt/e/data/Crick/PDS_Diagnostics_2020/PDS2021318subset";
Logger.Log.Debug("AssembleSamples: " + AppConfigHelper.LastUser + " CMD: " + AppConfigHelper.LastCommand);
RunInBackground(AppConfigHelper.LastCommand, AppConfigHelper.LastTaskID);
WSLProxyResponse WSLResponse = new WSLProxyResponse();
WSLResponse.ExitCode = 0;
return(WSLResponse);
}
public static WSLProxyResponse BuildTree()
{
//string prefix = "cd;export PATH=/home/arnie/.local/bin:/home/arnie/bin:/snap/bin:/home/arnie/.dotnet/tools:$PATH;conda run -n phame "; // Prepend to each invocation of wsl.
//prefix = "conda run -n phame ";
// eg. seqdb build_tree -n 50 -t 1 –fast_tree -l query.list -r reference.fasta -o path/to/output_dir -d path/to/seqdb_database.
// First we need to build a file containing the contents of the query list.
List <string> checkedQueries = new List <string>();
string[] queryList = AppConfigHelper.BuildTreeQueryList().ToArray();
for (int i = 0; i < queryList.Length; i++)
{
string s1 = queryList[i];
if (s1.StartsWith("1"))
{
checkedQueries.Add(AppConfigHelper.NormalizePathToLinux(s1.Substring(1))); // Remove 'selected' indicator.
}
}
queryList = checkedQueries.ToArray();
Array.Resize(ref queryList, queryList.Length + 1); // Add an empty line to give us a final LF.
queryList[queryList.Length - 1] = string.Empty;
File.WriteAllText(@"C:\Temp\queryList.txt", string.Join("\n", queryList));
if (File.Exists(AppConfigHelper.BuildTreeOutputPath() + "\\tree.nwk"))
{
File.Delete(AppConfigHelper.BuildTreeOutputPath() + "\\tree.nwk");
}
//int taskid = AppConfigHelper.MaxTaskID() + 1;
//BioSeqTask task = new BioSeqTask()
//{
// //TaskData = AppConfigHelper.BuildTreeOutputPath() + "\\tree.nwk",
// TaskDB = AppConfigHelper.CurrentDBName(),
// TaskID = taskid.ToString(),
// TaskStatus = "Pending",
// TaskTime = DateTime.Now,
// TaskComplete = DateTime.MinValue,
// TaskType = "BuildTree",
// TaskUser = AppConfigHelper.LastUser,
// StandardOutput = string.Empty,
// LastError = string.Empty,
// LastExitCode = -999
//};
//AppConfigHelper.AddTask(task);
//TaskID = task.TaskID;
string referenceToUse = AppConfigHelper.BuildTreeChooseDomestic ? AppConfigHelper.BuildTreeDomesticReference : AppConfigHelper.BuildTreeWildReference();
string linkage = string.Empty;
string cutoff = string.Empty;
switch (AppConfigHelper.BuildTreeLinkage)
{
case 0:
linkage = "threshold";
cutoff = " -c " + AppConfigHelper.BuildTreeThreshold;
break;
case 1:
linkage = "tophits";
cutoff = " -c " + AppConfigHelper.BuildTreeHits;
break;
case 2:
linkage = "cluster";
break;
}
WSLProxyResponse WSLResponse = new WSLProxyResponse();
WSLResponse.ExitCode = 0;
AppConfigHelper.LastCommand = AppConfigHelper.CondaPrefix() + " " + AppConfigHelper.PathToSeqDB() +
" build_tree " + (AppConfigHelper.BuildTreeFastTree() ? "--fast_tree " : string.Empty) +
"--linkage " + linkage + cutoff +
" -l " + AppConfigHelper.NormalizePathToLinux("C:\\Temp\\queryList.txt") +
" -r " + AppConfigHelper.NormalizePathToLinux(referenceToUse) +
" -t " + AppConfigHelper.BuildTreeThreads() +
" -d " + AppConfigHelper.NormalizePathToLinux(AppConfigHelper.CurrentDBPath()) +
" -o " + AppConfigHelper.NormalizePathToLinux(AppConfigHelper.BuildTreeOutputPath());
if (AppConfigHelper.BuildTreeFastTree()) // Submit and look for tree.nwk.
{
FileSystemWatcher _watcher = new FileSystemWatcher(AppConfigHelper.BuildTreeOutputPath());
_watcher.Created += _watcher_Created;
_watcher.Filter = "tree.nwk";
_watcher.EnableRaisingEvents = true;
AppConfigHelper.StandardOutput = string.Empty;
AppConfigHelper.LastError = string.Empty;
AppConfigHelper.LastExitCode = 0;
Logger.Log.Debug("BuildTree: " + AppConfigHelper.LastUser + " CMD: " + AppConfigHelper.LastCommand);
var info = new ProcessStartInfo(AppConfigHelper.PathToWSL(), "bash -ic '" + AppConfigHelper.CondaPrefix() + " " + AppConfigHelper.LastCommand + " &> " +
AppConfigHelper.LinuxHomeDirectory + "/output" + AppConfigHelper.LastTaskID.ToString() + "'")
{
WorkingDirectory = AppConfigHelper.NormalizePathToWindows(AppConfigHelper.LinuxHomeDirectory),
UseShellExecute = false,
CreateNoWindow = true,
RedirectStandardInput = true,
RedirectStandardOutput = true,
RedirectStandardError = true
};
Process P = Process.Start(info);
WSLResponse.StandardError = P.StandardError.ReadToEnd();
WSLResponse.StandardOutput = P.StandardOutput.ReadToEnd();
}
else
{
RunInBackground(AppConfigHelper.LastCommand, AppConfigHelper.LastTaskID);
}
return(WSLResponse);
}