bugfix-test-10

Changes

@@ -1,3 +1,11 @@
+0.8.2   2023-11-08
+
+* Bugfix: test 10-hpc had a typo and didnt work on Slurm clusters
+
+0.8.1  2023-10-13
+
+* Bugfix on stderr file name automatically assigned
+
 0.8.0  2023-10-12
 
 * Improved `runjob` verbose output and automatic naming

bin/make_image_from_bioconda

@@ -9,7 +9,7 @@ use Pod::Usage;
 use Term::ANSIColor qw(:constants);
 use NBI::Slurm;
 
-my $config = NBI::Slurm::load_config("$USER/.nbislurm.config");
+my $config = NBI::Slurm::load_config("$ENV{USER}/.nbislurm.config");
 my $output  = undef;
 my $move   = 0;
 my $def_file = undef;

bin/make_package

@@ -11,7 +11,7 @@ use File::Spec;
 use Pod::Usage;
 use NBI::Slurm;
 
-my $config    = NBI::Slurm::load_config("$USER/.nbislurm.config");
+my $config    = NBI::Slurm::load_config("$ENV{USER}/.nbislurm.config");
 my $image     = undef;
 my $package   = undef;
 my $force     = 0;
@@ -80,9 +80,8 @@ if (chmod($permissions, $source_file)) {
 # Create symbolic links for the provided commands
 my @COMMANDS = `singularity exec \"$image\" cat /etc/binaries.txt`;
 if ($? != 0) {
-    say STDERR "ERROR: Failed to read /etc/binaries.txt from image.";
-    say STDERR "  -> Are you sure this is a valid Singularity image?";
-    exit 1;
+    say STDERR "WARNING: Failed to read /etc/binaries.txt from image.";
+    say STDERR "  -> We will consider this a 'custom' Singularity image?";
 } elsif (scalar @COMMANDS == 0) {
     say STDERR "ERROR: No commands supplied (or no /etc/binaries.txt found).";
 } else {

bin/runjob

@@ -63,6 +63,16 @@ $queue = update_queue($queue, $time_hours);
 $command = join(" ", @ARGV);
 usage(1) unless ($command);
 
+if ($verbose) {
+    say STDERR YELLOW, BOLD, "PARAMETERS:",RESET;
+    say STDERR YELLOW, "Queue:      ", RESET, $queue // "(not set)";
+    say STDERR YELLOW, "Memory:     ", RESET, $memory // "(not set)";
+    say STDERR YELLOW, "Threads:    ", RESET, $threads // "(not set)";
+    say STDERR YELLOW, "Time:       ", RESET, $time // "(not set)";
+    say STDERR YELLOW, "Tmpdir:     ", RESET, $tmpdir // "(not set)";
+    say STDERR YELLOW, "Name:       ", RESET, $name // "(not set)";
+    say STDERR YELLOW, "Command:    ", RESET, $command // "(not set)";
+}
 # Check threadshours
 if (-d $time) {
     say STDERR RED, BOLD, "ERROR:", RESET, " did you mean \"--tmpdir $time\"  instead of $threads threads?";

lib/NBI/Job.pm

@@ -9,8 +9,8 @@ use File::Spec::Functions;
 $Data::Dumper::Sortkeys = 1;
 use File::Basename;
 
-$NBI::Job::VERSION           = $NBI::Slurm::VERSION;
-my $DEFAULT_QUEUE               = "nbi-short";
+$NBI::Job::VERSION  = $NBI::Slurm::VERSION;
+my $DEFAULT_QUEUE   = "nbi-short";
 require Exporter;
 our @ISA = qw(Exporter);
 
@@ -156,7 +156,7 @@ sub errorfile : lvalue {
 
     # Create a default error_file if not defined
     if (not defined $self->{error_file}) {
-        $self->{error_file} = catfile( $self->opts->tmpdir , $self->name . ".%j.out");
+        $self->{error_file} = catfile( $self->opts->tmpdir , $self->name . ".%j.err");
     }
 
     if ($interpolate) {
@@ -434,6 +434,11 @@ Accessor method for the error file path.
 
 This method allows you to get or set the path of the error file generated by the job. If called with an argument, it sets the error file path to the specified value. If called without an argument, it returns the current error file path.
 
+=head2 script_path
+
+Accessor method for the actual script path. This is the path of the script file generated by the job.
+invoking C<run()> will generate a script path if it was not set.
+
 =head2 append_command
 
 Append a command to the job.
@@ -507,4 +512,10 @@ Submit the job to SLURM.
   my $jobid = $job->run;
 
 This method submits the job to SLURM for execution. 
-It generates the sbatch script, writes it to a file, and uses the "sbatch" command to submit the job. If the submission is successful, it returns the job ID assigned by SLURM. Otherwise, it throws an exception.
+It generates the sbatch script, writes it to a file, and uses the "sbatch" command to submit the job. If the submission is successful, it returns the job ID assigned by SLURM. Otherwise, it throws an exception.
+
+=head2 view
+
+Return a string representation of the object.
+
+  my $str = $job->view;

lib/NBI/Slurm.pm

@@ -7,8 +7,8 @@ use NBI::Job;
 use NBI::Opts;
 use base qw(Exporter);
 our @ISA = qw(Exporter);
-our @EXPORT = qw(Job Opts load_config %FORMAT_STRINGS);
-$NBI::Slurm::VERSION = '0.8.0';
+our @EXPORT = qw(Job Opts load_config has_queue %FORMAT_STRINGS);
+$NBI::Slurm::VERSION = '0.8.1';
 
 
 

t/10-hpc.t

@@ -5,11 +5,15 @@ use Test::More;
 use Data::Dumper;
 use NBI::Slurm;
 
+my $has_queue = NBI::Slurm::has_squeue();
+
 # Skip if NBI::Slurm::has_squeue() is false
-if (NBI::Slurm::has_squeue() == 0) {
+if ($has_queue == 0) {
     plan skip_all => "Skipping all tests: not in a slurm cluster";
 }
 
-my @queue = NBI::Slurm::queue();
+ok($has_queue == 1, "has_squeue() returns a value");
+
+my @queue = NBI::Slurm::queues();
 ok(scalar @queue > 0, "queue() returns a list of queues");
 done_testing();