Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/LICENSE
+++ b/LICENSE
 SPADES: SAINT-PETERSBURG GENOME ASSEMBLER
-Copyright (c) 2015-2017 Saint Petersburg State University
+Copyright (c) 2015-2018 Saint Petersburg State University
 Copyright (c) 2011-2014 Saint Petersburg Academic University

 SPAdes is free software; you can redistribute it and/or modify

--- a/VERSION
+++ b/VERSION
-3.11.1
+3.12.0
--- a/changelog.html
+++ b/changelog.html
@@ -3,6 +3,36 @@

 <h2>SPAdes Genome Assembler changelog</h2>

+<h3>SPAdes 3.12.0, 14 May 2018</h3>
+
+<p>NEW: Support for merged paired-end reads.</p>
+
+<p>NEW: Experimental pipeline for metagenome hybrid assemblies.</p>
+
+<p>NEW: Standalone graph builder application.</p>
+
+<p>NEW: Standalone k-mer counting application.</p>
+
+<p>NEW: Standalone long read to graph aligner.</p>
+
+<p>CHANGE: Significant improvements in hybrid assembly pipeline.</p>
+
+<p>CHANGE: Faster read alignment using BWA.</p>
+
+<p>CHANGE: Improvements in metaSPAdes results.</p>
+
+<p>CHANGE: More sensitive results for rnaSPAdes.</p>
+
+<p>CHANGE: All binaries for SPAdes pipeline steps now have <code>spades-</code> prefix in its name.</p>
+
+<p>CHANGE: Better running time and RAM consumption for graph construction stage.</p>
+
+<p>CHANGE: Overall performance improvements.</p>
+
+<p>FIX: K value estimation for rnaSPAdes.</p>
+
+<p>DEPRECATED: dipSPAdes pipeline for highly polymorphic diploid genomes (still present in the release but no longer supported).</p>
+
 <h3>SPAdes 3.11.1, 1 October 2017</h3>

 <p>FIX: Handling spaces in path during mismatch correction.</p>

--- a/configs/debruijn/careful_mda_mode.info
+++ b/configs/debruijn/careful_mda_mode.info
@@ -3,6 +3,7 @@ simp
    ; bulge remover:
    br
    {
+        enabled true
        max_relative_coverage		1.1	; bulge_cov < this * not_bulge_cov
    }
    

--- a/configs/debruijn/careful_mode.info
+++ b/configs/debruijn/careful_mode.info
@@ -3,6 +3,7 @@ simp
    ; bulge remover:
    br
    {
+        enabled true
        max_relative_coverage       0.5     ; bulge_cov < this * not_bulge_cov
        ; parallel false
    }

--- a/configs/debruijn/config.info
+++ b/configs/debruijn/config.info
@@ -78,10 +78,6 @@ paired_info_statistics false
 ; set it true to get statistics for pair information (over gaps), such as false positive/negative, perfect match, etc.
 paired_info_scaffolder false

-;FIXME is it always simple?
-estimation_mode simple
-; simple, weighted, extensive, smoothing
-
 ;the only option left from repeat resolving
 max_repeat_length 8000

@@ -123,8 +119,10 @@ gap_closer_enable   true
 gap_closer
 {
    minimal_intersection	10
-    before_simplify		true
-    in_simplify    		false
+
+    ;before_raw_simplify and before_simplify are mutually exclusive
+    before_raw_simplify    		true
+    before_simplify		false
    after_simplify 		true
    weight_threshold		2.0
 }
@@ -145,14 +143,11 @@ lcer

 pacbio_processor
 {
+    bwa_length_cutoff 200
 ;align and traverse.
-    pacbio_k 13
-    additional_debug_info false
    compression_cutoff 0.6
-    domination_cutoff 1.5
    path_limit_stretching 1.3
    path_limit_pressing 0.7
-    ignore_middle_alignment true
    max_path_in_dijkstra 15000
    max_vertex_in_dijkstra 2000
 ;gap_closer
@@ -172,10 +167,7 @@ graph_read_corr

 bwa_aligner
 {
-    ;stupid naming since spades.py cannot change config normally
-    bwa_enable false
    debug false
-    path_to_bwa ./bin/bwa-spades
    min_contig_len 0
 }


--- a/configs/debruijn/construction.info
+++ b/configs/debruijn/construction.info
@@ -11,6 +11,9 @@ construction
 	; size of buffer for each thread in MB, 0 for autodetection
 	read_buffer_size 0

+        ; read median coverage threshold
+        read_cov_threshold 0
+
 	early_tip_clipper
 	{
 		; tip clipper can be enabled only in extension mode

--- a/configs/debruijn/diploid_mode.info
+++ b/configs/debruijn/diploid_mode.info
@@ -2,8 +2,6 @@ mode diploid

 simp
 {
-    post_simplif_enabled false
-
 	; bulge remover:
 	br
 	{

--- a/configs/debruijn/distance_estimation.info
+++ b/configs/debruijn/distance_estimation.info
@@ -40,7 +40,3 @@ amb_de {
    relative_length_threshold       0.8
    relative_seq_threshold          0.5
 }
-
-sensitive_mapper {
-    k   19
-}
--- a/configs/debruijn/large_genome_mode.info
+++ b/configs/debruijn/large_genome_mode.info
+;FIXME do we still need this mode?
 mode large_genome

-
 pe {

 debug_output false
@@ -9,14 +9,3 @@ params {
    scaffolding_mode old_pe_2015
 }
 }
-
-
-bwa_aligner
-{
-    bwa_enable true
-    debug false
-    path_to_bwa ./bin/bwa-spades
-    min_contig_len 0
-}
-
-
--- a/configs/debruijn/log.properties
+++ b/configs/debruijn/log.properties
@@ -37,9 +37,10 @@ default=INFO

 #PathExtender=DEBUG
 #BidirectionalPath=DEBUG
-#NextPathSearcher=DEBUG
 #ExtensionChooser=DEBUG
-#WeightCounter=DEBUG
+#ExcludingExtensionChooser=DEBUG
+#SimpleExtensionChooser=DEBUG
+#WeightCounter=TRACE
 #PathExtendIO=DEBUG
 #PathExtendPI=DEBUG
 #LoopTraverser=DEBUG
@@ -52,6 +53,7 @@ default=INFO
 #ScaffoldingPathExtender=DEBUG
 #CoordCoverageExtensionChooser=DEBUG
 #SimpleCoverageExtensionChooser=DEBUG
+#IdealInfoProvider=TRACE

 #BWAPairInfo=TRACE
 #LongReadMapper=TRACE

--- a/configs/debruijn/mda_mode.info
+++ b/configs/debruijn/mda_mode.info
@@ -47,29 +47,6 @@ simp
        max_coverage_coeff  5.0
    }
    
-    tec
-    {
-        max_ec_length_coefficient   55  ; max_ec_length = k + max_ec_length_coefficient
-        uniqueness_length       1500
-        plausibility_length     200
-    }
-    
-    ; topology and reliability based erroneous connection remover
-    trec
-    {
-        max_ec_length_coefficient   100 ; max_ec_length = k + max_ec_length_coefficient
-        uniqueness_length       1500
-        unreliable_coverage     2.5
-    }
-    
-    ; topology tip clipper:
-    ttc
-    {
-        length_coeff    3.5
-        plausibility_length 250
-        uniqueness_length   1500
-    }
-
    ; complex bulge remover
    cbr
    {
@@ -114,8 +91,7 @@ params {
    ; extension selection
    extension_options
    {
-        use_default_single_threshold false
-        single_threshold           0.001
+        single_threshold           0.3
        weight_threshold           0.6
        max_repeat_length          8000
    }

--- a/configs/debruijn/meta_mode.info
+++ b/configs/debruijn/meta_mode.info
@@ -5,9 +5,6 @@ two_step_rr true
 ; enables/disables usage of intermediate contigs in two-step pipeline
 use_intermediate_contigs true

-;if true simple mismatches are corrected
-correct_mismatches          false
-
 ;flanking coverage range
 flanking_range 30

@@ -32,7 +29,7 @@ simp
    {
        ; rctc: tip_cov < rctc * not_tip_cov
        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
-        condition               "{ tc_lb 3.5, cb 1000000, rctc 2.0 } { tc_lb 6., cb 2.5, rctc 1.0 }"
+        condition               "{ rl 0.2 } { rlmk 2., rctc 2.0 }"
    }

    ; relative coverage erroneous component remover:
@@ -54,15 +51,17 @@ simp
    }
    
    ; relative edge disconnector:
-    relative_ed
+    red
    {
        enabled true
        diff_mult  5.
+        unconditional_diff_mult 50.
    }

    ; bulge remover:
    br
    {
+        enabled true
        max_coverage			1000000.0
        max_relative_coverage		5.		; bulge_cov < this * not_bulge_cov
        max_delta			10
@@ -74,9 +73,7 @@ simp
    ; final tip clipper:
    final_tc
    {
-        ; rctc: tip_cov < rctc * not_tip_cov
-        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
-        condition               "{ lb 500, cb 3., rctc 0.7 } { lb 1500, cb 20., rctc 0.2 }"
+        condition               "{ lb 500, rctc 0.4 } { lb 850, rctc 0.2 }"
    }

    ; final bulge remover:
@@ -84,17 +81,24 @@ simp
    {
        enabled true
        main_iteration_only true
-        max_bulge_length_coefficient    50.     ; max_bulge_length = max_bulge_length_coefficient * k
+        max_bulge_length_coefficient    30.     ; max_bulge_length = max_bulge_length_coefficient * k
        max_coverage			1000000.0
        max_relative_coverage       0.5     ; bulge_cov < this * not_bulge_cov
-        max_delta           50
+        max_delta           45
        max_relative_delta		0.1
    }

+    ; complex bulge remover
+    cbr
+    {
+        enabled true
+    }
+
    ; hidden ec remover
    her
    {
-        enabled                     true
+        ; TODO NB config used in special meta mode version (always enabled)
+        enabled                     false
        uniqueness_length           1500
        unreliability_threshold     -1.
        relative_threshold          3.     
@@ -102,43 +106,49 @@ simp

    init_clean
    {
-       early_it_only   true
-       ier {
+        activation_cov  -1.
+        early_it_only   false
+        ier
+        {
            enabled true
        }
-       tip_condition   "{ tc_lb 3.5, cb 2.0 }"
-       ec_condition    "{ ec_lb 10, cb 0.5 }"
+        ;Disable if it does not help the br performance much!
+        tip_condition   "{ tc_lb 3.5, cb 2.1 }"
+        ;ec_condition is here only to speed-up future br on early iterations
+        ec_condition    "{ ec_lb 10, cb 1.5 }"
+        disconnect_flank_cov    -1.
    }

 }

-;FIXME rename
+;TODO rename
 preliminary_simp
 {
    init_clean
    {
-        self_conj_condition "{ ec_lb 100, cb 20.0 }"
-        early_it_only   false
-        ier
-        {
-            enabled true
-        }
-        tip_condition   "{ rlmk, cb 1.2, mmm 2 }"
+        tip_condition   "loop 2 { rlmk 1., cb 1.2, mmm 2 } { rlmk 1., cb 1.2, mmm 0.05 } { rl 0.2, cb 1.2 }"
        ec_condition    "{ ec_lb 0, cb 0.9 }"
        disconnect_flank_cov    0.8
    }

-    post_simplif_enabled false
-
    ; bulge remover:
    br
    {
+        enabled true
        max_coverage			1000000.0
        max_relative_coverage		0.5		; bulge_cov < this * not_bulge_cov
        max_delta			10
        max_relative_delta		0.1
    }

+    ; Currently will not work even if enabled. Left for experiments.
+    ; relative edge disconnector
+    red
+    {
+        enabled false
+        diff_mult  10.
+        unconditional_diff_mult 100.
+    }
 }

 ; undo single cell config changes, enforce filtering
@@ -174,7 +184,6 @@ params {
    ; extension selection
    extension_options
    {
-        use_default_single_threshold true
        single_threshold           0.3
        weight_threshold           0.6
        priority_coeff             1.5

--- a/configs/debruijn/moleculo_mode.info
+++ b/configs/debruijn/moleculo_mode.info
@@ -16,6 +16,7 @@ simp
    ; bulge remover:
    br
    {
+        enabled true
        max_coverage            3
        max_relative_coverage       100000.     ; bulge_cov < this * not_bulge_cov
    }
@@ -41,29 +42,6 @@ simp
        max_coverage_coeff  5.0
    }
    
-    tec
-    {
-        max_ec_length_coefficient   55  ; max_ec_length = k + max_ec_length_coefficient
-        uniqueness_length       1500
-        plausibility_length     200
-    }
-    
-    ; topology and reliability based erroneous connection remover
-    trec
-    {
-        max_ec_length_coefficient   100 ; max_ec_length = k + max_ec_length_coefficient
-        uniqueness_length       1500
-        unreliable_coverage     2.5
-    }
-    
-    ; topology tip clipper:
-    ttc
-    {
-        length_coeff    3.5
-        plausibility_length 250
-        uniqueness_length   1500
-    }
-
    ; complex bulge remover
    cbr
    {
@@ -85,8 +63,6 @@ simp

    init_clean
    {
-        early_it_only   true
-
        activation_cov  -1.
        ier
        {
@@ -112,8 +88,7 @@ params {
    ; extension selection
    extension_options
    {
-        use_default_single_threshold false
-        single_threshold           0.001
+        single_threshold           0.3
        weight_threshold           0.6
    }


--- a/configs/debruijn/pe_params.info
+++ b/configs/debruijn/pe_params.info
@@ -25,13 +25,11 @@ params {
        cut_all false
    }

-    split_edge_length    99
    normalize_weight     true
    
    ; extension selection
    extension_options
    {
-        use_default_single_threshold true
        single_threshold           0.1
        weight_threshold           0.5
        priority_coeff             1.5
@@ -41,7 +39,6 @@ params {

    mate_pair_options
    {
-        use_default_single_threshold true
        single_threshold           30
        weight_threshold           0.5
        priority_coeff             1.5

--- a/configs/debruijn/rna_mode.info
+++ b/configs/debruijn/rna_mode.info
@@ -8,7 +8,6 @@ strand_specificity {
    antisense false
 }

-
 contig_output {
    scaffolds_name  transcripts
    ; none  --- do not output broken scaffolds | break_gaps --- break only by N steches | break_all --- break all with overlap < k
@@ -17,24 +16,26 @@ contig_output {

 simp
 {
-    ; enable advanced ec removal algo
+    ;all topology based erroneous connection removers are off
    topology_simplif_enabled false
+
    tc
    {
        ; rctc: tip_cov < rctc * not_tip_cov
        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
-        condition  "{ mmm 3 tc_lb 3.5, cb 100000, rctc 0.1 } { tc_lb 3.5, cb 4, rctc 10000 } { tc_lb 0.1, cb 20, rctc 10000 }"
+        condition  "{ mmm 3 tc_lb 4, cb 100000, rctc 0.5 } { tc_lb 2, cb 1, rctc 10000 }"
    }

    dead_end
    {
-        condition  "{ tc_lb 3.5, cb 2 }"
        enabled true
+        condition  "{ tc_lb 3.5, cb 2 }"
    }

    ; bulge remover:
    br
    {
+        enabled true
        max_additive_length_coefficient 100
        max_coverage            1000000.0
        max_relative_coverage       100000.0 ; bulge_cov < this * not_bulge_cov
@@ -55,48 +56,29 @@ simp
    rcec
    {
        enabled true
-            rcec_lb 30
-            rcec_cb 0.5
    }

    rcc
    {
        enabled true
        coverage_gap    20.
-        max_length_coeff    2.0
-        max_length_with_tips_coeff   3.0
-        max_vertex_cnt      30
-        max_ec_length_coefficient   30
-        max_coverage_coeff  5.0
-    }
-
-    ;all topology based erroneous connection removers are off
-    ier
-    {
-        enabled                     false
    }

    ; hidden ec remover
    her
    {
-        enabled                     true
+        ; TODO NB config also used in special rna mode version (always enabled)
+        enabled                     false
        uniqueness_length           1500
        unreliability_threshold     0.2
        relative_threshold          5
    }

-    init_clean
-    {
-        activation_cov  -1.
    ier
    {
        enabled                     false
    }

-        tip_condition   ""
-        ec_condition    ""
-    }
-
 }

 ; disable filtering in rna mode
@@ -121,15 +103,14 @@ params {

    extension_options
    {
-        use_default_single_threshold true
        single_threshold           0.05
    }

    scaffolder {
        cutoff        1
-        hard_cutoff   10
+        hard_cutoff   5
        cluster_info false
-        min_overlap_for_rna_scaffolding 10
+        min_overlap_for_rna_scaffolding 8
    }

    path_cleaning_presets "default soft hard"

--- a/configs/debruijn/simplification.info
+++ b/configs/debruijn/simplification.info
@@ -2,14 +2,38 @@

 simp
 {
-    ; number of iterations in basic simplification cycle
-    cycle_iter_count 10
+    ; ==== RAW SIMPLIFICATION ==== 
+    init_clean
+    {
+        self_conj_condition "{ ec_lb 100, cb 1.0 }"
+        early_it_only   false
+        ; will be enabled only if average coverage >= activate_cov
+        ; if value < 0 check not performed
+        activation_cov  10.

-    ; enable advanced simplification algo
-    post_simplif_enabled true
+        ; isolated edges remover
+        ier
+        {
+            enabled                     true
+            use_rl_for_max_length         false ; max_length will be taken max with read_length
+            use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
+            max_length                  0 ; will be taken max with read_length if option above is set
+            max_coverage                0
+            max_length_any_cov          0 ; will be taken max with read_length if option above is set
+        }

-    ; enable advanced ec removal algo
-    topology_simplif_enabled false
+        tip_condition   "{ tc_lb 3.5, cb auto }"
+        ec_condition    "{ ec_lb 10, cb 2.0 }"
+
+        ; edges with flank cov around alternative less than value will be disconnected 
+        ; negative value to disable
+        disconnect_flank_cov    -1.0
+    }
+
+    ; ==== SIMPLIFICATION CYCLE ==== 
+
+    ; number of iterations in basic simplification cycle
+    cycle_iter_count 10

    ; tip clipper:
    tc
@@ -49,6 +73,13 @@ simp
       ; condition               "{ ec_lb 9, icb 40.0 }"
    }

+    dead_end {
+        enabled false
+        condition ""
+    }
+
+    ; ==== POST-SIMPLIFICATION ==== 
+
    ; relative coverage erroneous connections remover:
    rcec
    {
@@ -70,11 +101,12 @@ simp
    }
    
    ; relative edge disconnector:
-    relative_ed
+    red
    {
        enabled false
        diff_mult  20.
        edge_sum   10000
+        unconditional_diff_mult 0. ; 0. to disable
    }

    ; final tip clipper:
@@ -102,11 +134,52 @@ simp
        buff_cov_rel_diff 0.2
    }

+    ; complex tip clipper
+    complex_tc
+    {
+        enabled               false
+        max_relative_coverage -1
+        max_edge_len          100
+        condition             "{ tc_lb 3.5 }"
+    }  
+
+    ; complex bulge remover
+    cbr
+    {
+        enabled false
+        max_relative_length 5.
+        max_length_difference   5
+    }
+ 
+    ; isolated edges remover
+    ier
+    {
+        enabled                     true
+        use_rl_for_max_length         false ; max_length will be taken max with read_length
+        use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
+        max_length                  0 ; will be taken max with read_length if option above is set
+        max_coverage                2
+        max_length_any_cov          150 ; will be taken max with read_length if option above is set
+    }
+
+    ; hidden ec remover
+    her
+    {
+        enabled                     false
+        uniqueness_length           1500
+        unreliability_threshold     4
+        relative_threshold          5
+    }
+    
+    ; ==== ADVANCED EC REMOVAL ALGO ==== 
+    ; enable advanced ec removal algo
+    topology_simplif_enabled false
+    
    ; topology based erroneous connection remover
    tec
    {
        max_ec_length_coefficient   55  ; max_ec_length = k + max_ec_length_coefficient
-        uniqueness_length       5000
+        uniqueness_length       1500
        plausibility_length     200
    }

@@ -135,23 +208,6 @@ simp
        plausibility_length     200
    }

-    piec
-    {
-        max_ec_length_coefficient   30  ; max_ec_length = k + max_ec_length_coefficient
-        min_neighbour_length        100
-    }
-
-    ; isolated edges remover
-    ier
-    {
-        enabled                     true
-        use_rl_for_max_length         false ; max_length will be taken max with read_length
-        use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
-        max_length                  0 ; will be taken max with read_length if option above is set
-        max_coverage                2
-        max_length_any_cov          150 ; will be taken max with read_length if option above is set
-    }
-    
    ; topology tip clipper:
    ttc
    {
@@ -160,60 +216,4 @@ simp
        uniqueness_length   1500
    }

-    ; complex tip clipper
-    complex_tc
-    {
-        enabled               false
-        max_relative_coverage -1
-        max_edge_len          100
-        condition             "{ tc_lb 3.5 }"
-    }  
-
-    ; complex bulge remover
-    cbr
-    {
-        enabled false
-        max_relative_length 5.
-        max_length_difference   5
-    }
-
-    ; hidden ec remover
-    her
-    {
-        enabled false
-        uniqueness_length           1500
-        unreliability_threshold     4
-        relative_threshold          5     
-    }
-
-    init_clean
-    {
-        self_conj_condition "{ ec_lb 100, cb 1.0 }"
-        early_it_only   false
-       ; will be enabled only if average coverage \leq activate_cov
-        activation_cov  10.
-
-        ; isolated edges remover
-        ier
-        {
-            enabled                     true
-            use_rl_for_max_length         false ; max_length will be taken max with read_length
-            use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
-            max_length                  0 ; will be taken max with read_length if option above is set
-            max_coverage                0
-            max_length_any_cov          0 ; will be taken max with read_length if option above is set
-        }
-
-        tip_condition   "{ tc_lb 3.5, cb auto }"
-        ec_condition    "{ ec_lb 10, cb 2.0 }"
-        ; edges with flank cov around alternative less than value will be disconnected 
-        ; negative value to disable
-        disconnect_flank_cov    -1.0
-    }
-
-    dead_end {
-        enabled false
-        condition ""
-    }
-    
 }
--- a/debian/changelog
+++ b/debian/changelog
+spades (3.12.0+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Fix watch file
+  * Standards-Version: 4.1.5
+
+ -- Andreas Tille <tille@debian.org>  Wed, 18 Jul 2018 07:49:49 +0200
+
 spades (3.11.1+dfsg-2) unstable; urgency=medium

  * Build-Depends: libnlopt-cxx-dev

--- a/debian/control
+++ b/debian/control
@@ -26,7 +26,7 @@ Build-Depends: debhelper (>= 11~),
               bwa,
               libbwa-dev,
               lynx
-Standards-Version: 4.1.4
+Standards-Version: 4.1.5
 Vcs-Browser: https://salsa.debian.org/med-team/spades
 Vcs-Git: https://salsa.debian.org/med-team/spades.git
 Homepage: http://cab.spbu.ru/software/spades/

--- a/debian/patches/0002_use_debian_packaged_python-joblib.patch
+++ b/debian/patches/0002_use_debian_packaged_python-joblib.patch
@@ -9,7 +9,7 @@ Description: We are using Debian packaged python-joblib

 --- a/src/spades_pipeline/hammer_logic.py
 +++ b/src/spades_pipeline/hammer_logic.py
-@@ -42,10 +42,13 @@
+@@ -46,10 +46,13 @@ def compress_dataset_files(dataset_data,
                 support.sys_call([pigz_path, '-f', '-7', '-p', str(max_threads), reads_file], log)
         else:
             addsitedir(ext_python_modules_home)
@@ -29,7 +29,7 @@ Description: We are using Debian packaged python-joblib
             for output in outputs:
 --- a/src/spades_pipeline/lucigen_nxmate.py
 +++ b/src/spades_pipeline/lucigen_nxmate.py
-@@ -43,12 +43,14 @@
+@@ -43,12 +43,14 @@ except ImportError:
     support.error("Can't process Lucigen NxMate reads! Python module regex is not installed!")
 
 addsitedir(spades_init.ext_python_modules_home)