[DO NOT MERGE] Detach kmer mapper

.github/workflows/basic.yml

@@ -181,6 +181,11 @@ jobs:
         run: >
           $INSTALL_DIR/$PKG_LINUX/bin/spades.py --test --grid-engine=mpi
 
+      - name: 'slurm configs only'
+        run: >
+          $INSTALL_DIR/$PKG_LINUX/bin/spades.py --test --grid-engine=slurm --only-generate-config --grid-extra=\"--gres=gpu:0\"
+
+
   build-mac:
     strategy:
       matrix:

src/common/alignment/kmer_mapper.hpp

@@ -161,7 +161,7 @@ class KmerMapper : public omnigraph::GraphActionHandler<Graph> {
     }
 
     Kmer Substitute(const Kmer &kmer) const {
-        VERIFY(this->IsAttached());
+        // VERIFY(this->IsAttached());
         const auto *rawval = mapping_.find(kmer);
         if (rawval == nullptr)
             return kmer;

src/common/pipeline/graph_pack_helpers.cpp

@@ -49,7 +49,7 @@ void EnsureIndex(GraphPack& gp) {
 void EnsureBasicMapping(GraphPack& gp) {
     auto &kmer_mapper = gp.get_mutable<KmerMapper<Graph>>();
 
-    VERIFY(kmer_mapper.IsAttached());
+    // VERIFY(kmer_mapper.IsAttached());
     EnsureIndex(gp);
     INFO("Normalizing k-mer map. Total " << kmer_mapper.size() << " kmers to process");
     kmer_mapper.Normalize();

src/projects/spades/pipeline.cpp

@@ -252,7 +252,7 @@ void assemble_genome() {
                                             cfg::get().flanking_range,
                                             cfg::get().pos.max_mapping_gap,
                                             cfg::get().pos.max_gap_diff);
-    if (cfg::get().need_mapping) {
+    if (0 && cfg::get().need_mapping) {
         INFO("Will need read mapping, kmer mapper will be attached");
         conj_gp.get_mutable<debruijn_graph::KmerMapper<debruijn_graph::Graph>>().Attach();
     }

src/projects/spades/pipeline/spades_pipeline/executors/executor_slurm.py

@@ -7,7 +7,7 @@
 ############################################################################
 import sys
 
-import executor_base
+from . import executor_base
 from ..options_storage import OptionStorage
 from .. import support