From aa19a92e4b93c21fc65fe9b8413243f48fef9c1c Mon Sep 17 00:00:00 2001
From: Fabio Sanchez <fabio.b.sanchez@gmail.com>
Date: Mon, 8 Jul 2024 20:24:27 -0300
Subject: [PATCH] updated: spades from 3.15.3 to 3.15.5 (fix
 https://github.com/ablab/spades/issues/873)

---
 .gitignore                          |  1 +
 build.sh                            |  0
 how-to-build.txt                    |  6 +++---
 others/docker/environment-base.lock | 22 +++++++++++-----------
 run-magset.sh                       |  2 +-
 wiki/How-to-install.md              |  4 ++--
 6 files changed, 18 insertions(+), 17 deletions(-)
 mode change 100644 => 100755 build.sh

diff --git a/.gitignore b/.gitignore
index 811d2e3..75baf65 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 /target/
 /dependency-reduced-pom.xml
 /magset-1.3.0.simg
+tests/
diff --git a/build.sh b/build.sh
old mode 100644
new mode 100755
diff --git a/how-to-build.txt b/how-to-build.txt
index 21fc38d..73845d0 100644
--- a/how-to-build.txt
+++ b/how-to-build.txt
@@ -1,10 +1,10 @@
 #To build the code and generate new docker image:
-./build.sh fsanchez/magset:1.5.0
+./build.sh fsanchez/magset:1.5.1
 
 #to update the remote image:
-#docker push fsanchez/magset:1.5.0
+#docker push fsanchez/magset:1.5.1
 
 (beta)
 #To generate the singularity image, please execute:
-singularity pull docker://fsanchez/magset:1.5.0
+singularity pull docker://fsanchez/magset:1.5.1
 
diff --git a/others/docker/environment-base.lock b/others/docker/environment-base.lock
index a823ee2..ccb8d99 100644
--- a/others/docker/environment-base.lock
+++ b/others/docker/environment-base.lock
@@ -47,12 +47,12 @@ https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.5.0-h924138e_1.tar.bz2#
 https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed
 https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-hec16e2b_4.tar.bz2#0f8b880d727df321ac70a224c18690cb
 https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2#b4a4381d54784606820704f7b5f05a15
+https://conda.anaconda.org/conda-forge/linux-64/libidn11-1.34-h1cef754_0.tar.bz2#80ec3a09ce5c0b1d32c0a137c89db257
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
 https://conda.anaconda.org/bioconda/linux-64/prank-v.170427-h9f5acd7_5.tar.bz2#aea43532dd04620f1abaf08146c89892
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.12-h166bdaf_2.tar.bz2#8302381297332ea50532cf2c67961080
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4acfc691e64342b9dae57cf2adc63238
-https://conda.anaconda.org/conda-forge/linux-64/libidn11-1.34-h1cef754_0.tar.bz2#80ec3a09ce5c0b1d32c0a137c89db257
-https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908
 https://conda.anaconda.org/conda-forge/linux-64/metis-5.1.0-h58526e2_1006.tar.bz2#d099b812378b1e133c12e3b75167d83a
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.9-h7f98852_0.tar.bz2#bf6f803a544f26ebbdc3bfff272eb179
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
@@ -119,10 +119,10 @@ https://conda.anaconda.org/bioconda/noarch/perl-devel-stacktrace-2.04-pl5321hdfd
 https://conda.anaconda.org/bioconda/linux-64/perl-url-encode-0.03-pl5321h9ee0642_0.tar.bz2#ae808218ba4a3eb830f03e4277ba4625
 https://conda.anaconda.org/conda-forge/linux-64/perl-data-dumper-2.183-pl5321h166bdaf_0.tar.bz2#bc64b4d3f071a6a9db2023e696a0a2cb
 https://conda.anaconda.org/conda-forge/linux-64/perl-mime-base64-3.16-pl5321h166bdaf_0.tar.bz2#ea00137633c45f99a5c0fdaa3418c507
+https://conda.anaconda.org/conda-forge/noarch/perl-common-sense-3.75-pl5321hd8ed1ab_0.tar.bz2#ef70dc77e8b10bbb62f5e843b401ef0e
 https://conda.anaconda.org/conda-forge/noarch/perl-exporter-5.74-pl5321hd8ed1ab_0.tar.bz2#fd2eac4e35f8c970870a3961c1df3e29
 https://conda.anaconda.org/conda-forge/linux-64/perl-scalar-list-utils-1.63-pl5321h166bdaf_0.tar.bz2#c8d96f52c1e8de80663f2e11fbabfd0d
 https://conda.anaconda.org/conda-forge/linux-64/perl-compress-raw-zlib-2.202-pl5321h166bdaf_0.tar.bz2#66176366c49e2f70b3a764bc744b5010
-https://conda.anaconda.org/conda-forge/noarch/perl-common-sense-3.75-pl5321hd8ed1ab_0.tar.bz2#ef70dc77e8b10bbb62f5e843b401ef0e
 https://conda.anaconda.org/conda-forge/noarch/perl-algorithm-diff-1.201-pl5321hd8ed1ab_0.tar.bz2#4ec6c1ea1d18947663b8cdc5f63cb2bf
 https://conda.anaconda.org/bioconda/noarch/perl-digest-hmac-1.04-pl5321hdfd78af_0.tar.bz2#872d481415766335aea1abc5b4b0a16d
 https://conda.anaconda.org/conda-forge/linux-64/perl-db_file-1.858-pl5321h166bdaf_0.tar.bz2#73e039a6ab8fbaa8b574097b4fcdd599
@@ -152,8 +152,8 @@ https://conda.anaconda.org/conda-forge/linux-64/python-3.10.6-ha86cf86_0_cpython
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.37.1-pyhd8ed1ab_0.tar.bz2#1ca02aaf78d9c70d9a81a3bed5752022
 https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.0.9-h166bdaf_7.tar.bz2#1699c1211d56a23c66047524cd76796e
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.7.2-h7f98852_0.tar.bz2#12a61e640b8894504326aadafccbb790
-https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_openblas.tar.bz2#955d993f41f9354bf753d29864ea20ad
 https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-16_linux64_openblas.tar.bz2#20bae26d0a1db73f758fc3754cab4719
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_openblas.tar.bz2#955d993f41f9354bf753d29864ea20ad
 https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.83.1-h2283fc2_0.tar.bz2#2a10689a8be25009984735be9a2b26a9
 https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h3e49a29_2.tar.bz2#3b88f1d0fe2580594d58d7e44d664617
 https://conda.anaconda.org/conda-forge/linux-64/wget-1.20.3-ha35d2d1_1.tar.bz2#c990e108f39e1b43adf61e984360c9a1
@@ -164,10 +164,10 @@ https://conda.anaconda.org/bioconda/linux-64/perl-net-ssleay-1.74-0.tar.bz2#5a81
 https://conda.anaconda.org/bioconda/noarch/perl-tree-dag_node-1.32-pl5321hdfd78af_0.tar.bz2#09b05f575f3ae5f4a87003c857e3ad5d
 https://conda.anaconda.org/bioconda/noarch/perl-libxml-perl-0.08-pl5321hdfd78af_3.tar.bz2#1c365765ae910890ad8787ef53dab70c
 https://conda.anaconda.org/bioconda/noarch/perl-exception-class-1.45-pl5321hdfd78af_0.tar.bz2#5c3c97db8109bee156618a9931bdd893
+https://conda.anaconda.org/bioconda/noarch/perl-types-serialiser-1.01-pl5321hdfd78af_0.tar.bz2#cfc65753e827bbef80c00eaa395f6ae7
 https://conda.anaconda.org/conda-forge/noarch/perl-carp-1.50-pl5321hd8ed1ab_0.tar.bz2#bdddc03e28019b902da71b722f2288d7
 https://conda.anaconda.org/conda-forge/noarch/perl-file-path-2.18-pl5321hd8ed1ab_0.tar.bz2#e13e456f61b8261ba074c0aa93086afe
 https://conda.anaconda.org/bioconda/linux-64/perl-encode-3.19-pl5321hec16e2b_1.tar.bz2#b2925d6255f57feeb61b5fa04d99fbf3
-https://conda.anaconda.org/bioconda/noarch/perl-types-serialiser-1.01-pl5321hdfd78af_0.tar.bz2#cfc65753e827bbef80c00eaa395f6ae7
 https://conda.anaconda.org/bioconda/noarch/perl-text-diff-1.45-pl5321hdfd78af_1.tar.bz2#e9b9f91c7e44a671faa8fbf20cbdd6f6
 https://conda.anaconda.org/bioconda/noarch/perl-ntlm-1.09-pl5321hdfd78af_5.tar.bz2#dac95634eb35296b62569c77e2ceef5c
 https://conda.anaconda.org/bioconda/noarch/perl-bioperl-core-1.7.8-pl5321hdfd78af_1.tar.bz2#e627a38fe206468089dc73a0aafb6c8c
@@ -183,12 +183,13 @@ https://conda.anaconda.org/conda-forge/linux-64/brotli-1.0.9-h166bdaf_7.tar.bz2#
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-5.0.3-h7f98852_1004.tar.bz2#e9a21aa4d5e3e5f1aed71e8cefd46b6a
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.10-h7f98852_1003.tar.bz2#f59c1242cc1dd93e72c2ee2b360979eb
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h7f98852_1.tar.bz2#536cc5db4d0a3ba0630541aec064b5e4
-https://conda.anaconda.org/conda-forge/linux-64/arpack-3.7.0-hdefa2d7_2.tar.bz2#8763fe86163198ef1778d1d8d22bb078
-https://conda.anaconda.org/conda-forge/linux-64/suitesparse-5.10.1-h9e50725_1.tar.bz2#a3a685b5f9aeb890ed874502fe56accf
 https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de
+https://conda.anaconda.org/conda-forge/linux-64/suitesparse-5.10.1-h9e50725_1.tar.bz2#a3a685b5f9aeb890ed874502fe56accf
+https://conda.anaconda.org/conda-forge/linux-64/arpack-3.7.0-hdefa2d7_2.tar.bz2#8763fe86163198ef1778d1d8d22bb078
 https://conda.anaconda.org/conda-forge/linux-64/curl-7.83.1-h2283fc2_0.tar.bz2#8968421d2c89a6b89dfc28d283971de1
 https://conda.anaconda.org/bioconda/linux-64/entrez-direct-16.2-he881be0_1.tar.bz2#ff30142050ba583481215a6e1b3a5de0
 https://conda.anaconda.org/bioconda/noarch/perl-io-socket-ssl-2.074-pl5321hdfd78af_0.tar.bz2#848d5e23136422e87522336ba1865a5b
+https://conda.anaconda.org/bioconda/linux-64/perl-json-xs-2.34-pl5321h9f5acd7_5.tar.bz2#73c6dd8e7f7a6440cf1412112882c320
 https://conda.anaconda.org/bioconda/noarch/perl-lwp-mediatypes-6.04-pl5321hdfd78af_1.tar.bz2#386b035f45e9389e6e9b1a367fdd19bb
 https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-data-20210112.006-pl5321hd8ed1ab_0.tar.bz2#a70f08650ec3919ee5e599834f1349d3
 https://conda.anaconda.org/bioconda/noarch/perl-time-local-1.30-pl5321hdfd78af_0.tar.bz2#9d8b188186489efe61bc63fd4a2b8259
@@ -196,7 +197,6 @@ https://conda.anaconda.org/conda-forge/linux-64/perl-pathtools-3.75-pl5321h166bd
 https://conda.anaconda.org/conda-forge/noarch/perl-file-temp-0.2304-pl5321hd8ed1ab_0.tar.bz2#0a039c4fc36748942287ee10d0431515
 https://conda.anaconda.org/bioconda/noarch/perl-encode-locale-1.05-pl5321hdfd78af_7.tar.bz2#b431fde1d115040cf39bb54280a03dc8
 https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.106-pl5321h87f3376_1.tar.bz2#4c62c232fda31558e0eba91cc221d00d
-https://conda.anaconda.org/bioconda/linux-64/perl-json-xs-2.34-pl5321h9f5acd7_5.tar.bz2#73c6dd8e7f7a6440cf1412112882c320
 https://conda.anaconda.org/bioconda/noarch/perl-test-differences-0.69-pl5321hdfd78af_0.tar.bz2#1f7a9aa718798b8f9544d0a80dea3673
 https://conda.anaconda.org/bioconda/linux-64/perl-bio-samtools-1.43-pl5321h7132678_3.tar.bz2#a01c3a7c281f92e448cc75374eb5b211
 https://conda.anaconda.org/conda-forge/noarch/pip-22.2.2-pyhd8ed1ab_0.tar.bz2#0b43abe4d3ee93e82742d37def53a836
@@ -206,11 +206,11 @@ https://conda.anaconda.org/bioconda/linux-64/fastani-1.33-h0fdf51a_1.tar.bz2#490
 https://conda.anaconda.org/bioconda/linux-64/mash-2.3-ha9a2dd8_3.tar.bz2#272e9719f69a9846e49f8292b7f4c965
 https://conda.anaconda.org/conda-forge/linux-64/git-2.37.3-pl5321h04cb727_0.tar.bz2#dc8ab3aeec8666e16718e62334f12914
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.6-h3f2fef4_8.tar.bz2#a9acf5495a4a83786bb255cf2baeaa9c
+https://conda.anaconda.org/bioconda/noarch/perl-json-4.09-pl5321hdfd78af_0.tar.bz2#61530b75f2abe670d0b40fb2c703d674
 https://conda.anaconda.org/bioconda/noarch/perl-business-isbn-3.007-pl5321hdfd78af_0.tar.bz2#3cdaa3f73497365e08346443d81dac81
 https://conda.anaconda.org/bioconda/noarch/perl-http-date-6.05-pl5321hdfd78af_0.tar.bz2#5ce7de4ea806149915caa033a3bbc9cf
 https://conda.anaconda.org/bioconda/noarch/perl-xml-sax-1.02-pl5321hdfd78af_1.tar.bz2#2402f3f7aab47052aa38e00fe6a2de3d
 https://conda.anaconda.org/bioconda/noarch/perl-archive-tar-2.40-pl5321hdfd78af_0.tar.bz2#ef5f007762b5ad9425694104d7db4463
-https://conda.anaconda.org/bioconda/noarch/perl-json-4.09-pl5321hdfd78af_0.tar.bz2#61530b75f2abe670d0b40fb2c703d674
 https://conda.anaconda.org/bioconda/noarch/perl-test-most-0.37-pl5321hdfd78af_0.tar.bz2#fba1e55e28fc0530b94db9db5288cc1a
 https://conda.anaconda.org/bioconda/noarch/perl-bioperl-run-1.007003-pl5321hdfd78af_0.tar.bz2#5b7b092efda407c9af1981426d83f3f5
 https://conda.anaconda.org/conda-forge/noarch/entrypoints-0.4-pyhd8ed1ab_0.tar.bz2#3cf04868fee0a029769bd41f4b2fbf2d
@@ -223,7 +223,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.2.1-pyhd8ed1ab_0.tar.bz2
 https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha2e5f31_6.tar.bz2#2a7de29fb590ca14b5243c4c812c8025
 https://conda.anaconda.org/bioconda/noarch/dendropy-4.5.2-pyh3252c3a_0.tar.bz2#3b762d50e12b28d30e5f58c832137ed6
 https://conda.anaconda.org/conda-forge/noarch/tenacity-8.0.1-pyhd8ed1ab_0.tar.bz2#8b29b2c12cb21dbd057755e5fd22d005
-https://conda.anaconda.org/bioconda/linux-64/spades-3.15.3-h95f258a_0.tar.bz2#11ff8c55cc166d98efa1f936f6c9e975
+https://conda.anaconda.org/bioconda/linux-64/spades-3.15.5-h95f258a_1.tar.bz2#62ab35497479905dce6860525262104f
 https://conda.anaconda.org/conda-forge/noarch/idna-3.3-pyhd8ed1ab_0.tar.bz2#40b50b8b030f5f2f22085c062ed013dd
 https://conda.anaconda.org/conda-forge/noarch/pkgutil-resolve-name-1.3.10-pyhd8ed1ab_0.tar.bz2#89e3c7cdde7d3aaa2aee933b604dd07f
 https://conda.anaconda.org/conda-forge/noarch/joblib-1.1.0-pyhd8ed1ab_0.tar.bz2#07d1b5c8cde14d95998fd4767e1e62d2
@@ -254,8 +254,8 @@ https://conda.anaconda.org/conda-forge/linux-64/cffi-1.15.1-py310h255011f_0.tar.
 https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.2-py310h5764c6d_0.tar.bz2#6ac13c26fe4f9d8d6b38657664c37fd3
 https://conda.anaconda.org/conda-forge/linux-64/simplejson-3.17.6-py310h5764c6d_1.tar.bz2#3374b66ff84cf3d5a542768a2ee3902c
 https://conda.anaconda.org/conda-forge/linux-64/python-igraph-0.9.11-py310hb58d747_0.tar.bz2#b83a85da0dbaf6da66007b881767dc05
-https://conda.anaconda.org/conda-forge/linux-64/peewee-3.15.1-py310hba2f8c6_0.tar.bz2#e563f33340d73f2df92f4bbb2203ed4a
 https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.4-py310hbf28c38_0.tar.bz2#8dc3e2dce8fa122f8df4f3739d1f771b
+https://conda.anaconda.org/conda-forge/linux-64/peewee-3.15.1-py310hba2f8c6_0.tar.bz2#e563f33340d73f2df92f4bbb2203ed4a
 https://conda.anaconda.org/conda-forge/linux-64/pyrsistent-0.18.1-py310h5764c6d_1.tar.bz2#d6bf97f14e0cc9d2024cf66b11bb79b8
 https://conda.anaconda.org/conda-forge/linux-64/llvmlite-0.38.1-py310h58363a5_0.tar.bz2#32f924efe5e677b4f2378d391d006199
 https://conda.anaconda.org/conda-forge/linux-64/intbitset-2.4.1-py310h5764c6d_3.tar.bz2#b8de5c1f1a6973dfab2a061427efa5f3
diff --git a/run-magset.sh b/run-magset.sh
index 4428aba..01726c6 100644
--- a/run-magset.sh
+++ b/run-magset.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 set -e
 
-version=1.5.0
+version=1.5.1
  
 function prop {
     grep "^${1}" ${file}|cut -d'=' -f2
diff --git a/wiki/How-to-install.md b/wiki/How-to-install.md
index 8057f67..9ab69b5 100644
--- a/wiki/How-to-install.md
+++ b/wiki/How-to-install.md
@@ -13,9 +13,9 @@
 <h1>Installing </h1>
 
 * Download the main script <br/>
-`curl -OL https://github.com/LaboratorioBioinformatica/magset/releases/download/1.5.0/run-magset.sh`
+`curl -OL https://github.com/LaboratorioBioinformatica/magset/releases/download/1.5.1/run-magset.sh`
 <br/> or <br/>
-`wget https://github.com/LaboratorioBioinformatica/magset/releases/download/1.5.0/run-magset.sh`
+`wget https://github.com/LaboratorioBioinformatica/magset/releases/download/1.5.1/run-magset.sh`
 * Make the script executable <br/>
 `chmod +x run-magset.sh`