private void stdAnalysesList_SelectedIndexChanged(object sender, EventArgs e)
{
if (stdRunsList.SelectedIndex > -1)
{
Properties.Settings.Default.platform = global.ssh_type;
Properties.Settings.Default.run = stdRunsList.SelectedItem.ToString();
settings SF = new settings();
SF.ShowDialog();
run_cmd = new StringBuilder();
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.run))
{
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.platform))
{
// run_cmd.Append("minion -p ").Append(Properties.Settings.Default.platform);
run_cmd.Append("minion -p ").Append(Properties.Settings.Default.server_name);
}
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.chemistry))
{
run_cmd.Append(" -c ").Append(Properties.Settings.Default.chemistry);
}
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.aligner))
{
run_cmd.Append(" -a ").Append(Properties.Settings.Default.aligner);
}
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.variant_caller))
{
run_cmd.Append(" -v ").Append(Properties.Settings.Default.variant_caller);
}
if (Properties.Settings.Default.demultiplex == true)
{
run_cmd.Append(" -d");
}
if (Properties.Settings.Default.dual_index == true)
{
run_cmd.Append(" -m Y*,I8,I8,Y*");
}
else if (Properties.Settings.Default.dual_index == false)
{
run_cmd.Append(" -m Y*,I8,Y*");
}
if (Properties.Settings.Default.custom_trim == true)
{
run_cmd.Append(" --a1 ").Append(Properties.Settings.Default.f_adapter).Append(" --a2 ").Append(Properties.Settings.Default.r_adapter);
}
}
}
}
/// <summary>
/// File menu Tab
/// </summary>
private void settingsToolStripMenuItem_Click(object sender, EventArgs e)
{
if (stdRunsList.SelectedIndex > -1)
{
Properties.Settings.Default.platform = global.ssh_type;
Properties.Settings.Default.run = stdRunsList.SelectedItem.ToString();
settings SF = new settings();
SF.ShowDialog();
}
}
private void customExecuteBtn_Click(object sender, EventArgs e)
{
if (customExecuteBtn.Text == "WORKFLOW")
{
Properties.Settings.Default.type = "custom";
settings SF = new settings();
SF.ShowDialog();
run_cmd = new StringBuilder();
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.run))
{
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.platform))
{
// run_cmd.Append("minion -p ").Append(Properties.Settings.Default.platform);
run_cmd.Append("minion -p ").Append(Properties.Settings.Default.server_name);
}
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.chemistry))
{
run_cmd.Append(" -c ").Append(Properties.Settings.Default.chemistry).Append(" --ss ").Append(singlesamps.ToString(0, singlesamps.Length - 1));
}
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.aligner))
{
run_cmd.Append(" -a ").Append(Properties.Settings.Default.aligner);
}
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.variant_caller))
{
run_cmd.Append(" -v ").Append(Properties.Settings.Default.variant_caller);
}
if (Properties.Settings.Default.demultiplex == true)
{
run_cmd.Append(" -d");
}
if (Properties.Settings.Default.dual_index == true)
{
run_cmd.Append(" -m Y*,I8,I8,Y*");
}
else if (Properties.Settings.Default.dual_index == false)
{
run_cmd.Append(" -m Y*,I8,Y*");
}
if (Properties.Settings.Default.custom_trim == true)
{
run_cmd.Append(" --a1 ").Append(Properties.Settings.Default.f_adapter).Append(" --a2 ").Append(Properties.Settings.Default.r_adapter);
}
}
}
else if (customExecuteBtn.Text == "EXECUTE")
{
DialogResult dialogResult = MessageBox.Show("Ready to analyze " + Properties.Settings.Default.run + "? \r\n\n" + run_cmd.ToString(), "Minion - Checkpoint", MessageBoxButtons.YesNo, MessageBoxIcon.Question);
if (dialogResult == DialogResult.Yes)
{
global.run_date = DateTime.Now.ToString();
global.run_duration = "In Progress...";
startAnalysis();
runHistory();
ssh_command("analyze", global.ssh_host, global.ssh_usr, global.ssh_pass, run_cmd.ToString());
}
else if (dialogResult == DialogResult.No) { dialogResult = DialogResult.Cancel; }
}
else if (customExecuteBtn.Text == "CANCEL")
{
DialogResult dialogResult = MessageBox.Show("Are you sure you want to cancel analysis on " + Properties.Settings.Default.run + "?", "Minion - Important Message", MessageBoxButtons.YesNo, MessageBoxIcon.Question);
if (dialogResult == DialogResult.Yes)
{
while (true)
{
if (terminalThread.IsBusy)
{
run_cmd = new StringBuilder();
run_cmd.Append("kill -9 `ps aux | grep minion.py | awk '{print $2}'`]");
ssh_command("kill", global.ssh_host, global.ssh_usr, global.ssh_pass, run_cmd.ToString());
terminalThread.CancelAsync();
}
else break;
}
}
else if (dialogResult == DialogResult.No) { dialogResult = DialogResult.Cancel; }
}
}
private void customWorkflowBtn_Click(object sender, EventArgs e)
{
Properties.Settings.Default.type = "custom";
settings SF = new settings();
SF.ShowDialog();
run_cmd = new StringBuilder();
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.run))
{
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.platform))
{
// run_cmd.Append("minion -p ").Append(Properties.Settings.Default.platform);
run_cmd.Append("minion -p ").Append(Properties.Settings.Default.server_name);
}
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.chemistry))
{
run_cmd.Append(" -c ").Append(Properties.Settings.Default.chemistry).Append(" --ss ").Append(singlesamps.ToString(0, singlesamps.Length - 1));
}
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.aligner))
{
run_cmd.Append(" -a ").Append(Properties.Settings.Default.aligner);
}
if (!String.IsNullOrWhiteSpace(Properties.Settings.Default.variant_caller))
{
run_cmd.Append(" -v ").Append(Properties.Settings.Default.variant_caller);
}
if (Properties.Settings.Default.demultiplex == true)
{
run_cmd.Append(" -d");
}
if (Properties.Settings.Default.dual_index == true)
{
run_cmd.Append(" -m Y*,I8,I8,Y*");
}
else if (Properties.Settings.Default.dual_index == false)
{
run_cmd.Append(" -m Y*,I8,Y*");
}
if (Properties.Settings.Default.custom_trim == true)
{
run_cmd.Append(" --a1 ").Append(Properties.Settings.Default.f_adapter).Append(" --a2 ").Append(Properties.Settings.Default.r_adapter);
}
}
}
/// <summary>
/// File menu Tab
/// </summary>
private void settingsToolStripMenuItem_Click(object sender, EventArgs e)
{
settings SF = new settings();
SF.ShowDialog();
}
