Merge branch 'master' of https://github.com/vinuesa/get_phylomarkers

README.md

@@ -75,13 +75,13 @@ A [**preprint version is available on bioRxiv**](https://www.biorxiv.org/content
 ## Developers
 The code is developed and maintained by [Pablo Vinuesa](https://www.ccg.unam.mx/~vinuesa/) 
 at [CCG-UNAM, Mexico](https://www.ccg.unam.mx/) and 
-[Bruno Contreras-Moreira](https://digital.csic.es/cris/rp/rp02661/) 
- at [EEAD-CSIC, Spain](http://www.eead.csic.es/). It is released to the public domain under the GNU GPLv3 [license](./LICENSE).
+[Bruno Contreras-Moreira](https://www.eead.csic.es/home/staffinfo?Id=71) 
+ at [EEAD-CSIC, Spain](http://www.eead.csic.es/). It is released to the public domain under the GNU GPLv3 [license](./LICENSE.txt).
 
 ## Acknowledgements
 
 ### Personal
 We thank Alfredo J. Hernández and Víctor del Moral at CCG-UNAM for technical support with server administration.
 
 ### Funding
-We gratefully acknowledge the funding provided by [DGAPA-PAPIIT/UNAM](https://dgapa.unam.mx/index.php/impulso-a-la-investigacion/papiit) (grants IN201806-2, IN211814 and IN206318) and [CONACyT-Mexico](https://conacyt.mx/) (grants P1-60071, 179133 and A1-S-11242) to [Pablo Vinuesa](https://www.ccg.unam.mx/~vinuesa/), as well as the Fundación ARAID,Consejo  Superior  de Investigaciones Científicas (grant 200720I038 and Spanish MINECO (AGL2013-48756-R) to [Bruno Contreras-Moreira](https://digital.csic.es/cris/rp/rp02661).
+We gratefully acknowledge the funding provided by [DGAPA-PAPIIT/UNAM](https://dgapa.unam.mx/index.php/impulso-a-la-investigacion/papiit) (grants IN201806-2, IN211814 and IN206318) and [CONACyT-Mexico](https://conacyt.mx/) (grants P1-60071, 179133 and A1-S-11242) to [Pablo Vinuesa](https://www.ccg.unam.mx/~vinuesa/), as well as the Fundación ARAID,Consejo  Superior  de Investigaciones Científicas (grant 200720I038 and Spanish MINECO (AGL2013-48756-R) to [Bruno Contreras-Moreira](https://www.eead.csic.es/home/staffinfo?Id=71).

apt-install_R_dependencies.sh

@@ -1,5 +1,6 @@
 #!/usr/bin/env bash
 
+# Author: Pablo Vinuesa, CCG-UNAM; @pvinmex
 # 2022-07-02 # sudo and add-apt-repository --yes
 # Install R-packages on ubuntu with apt install
 
@@ -23,3 +24,6 @@ r-cran-stringr \
 r-cran-seqinr \
 r-cran-remotes \
 && sudo apt clean && apt purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+
+#NOTE: may need to install stringi as roow with install.packages("stringi", dep=T)

install_kdetrees_from_github.R

@@ -23,6 +23,6 @@ for (package in required_packages) {
 
 
 library("remotes")
-remotes::install_github("grady/kdetrees", dependencies = TRUE)
+remotes::install_github("grady/kdetrees", dependencies = TRUE, force = TRUE, upgrade="always")
 
 sessionInfo()

run_get_phylomarkers_pipeline.sh

@@ -4,7 +4,7 @@
 #: AUTHORS: Pablo Vinuesa, Center for Genome Sciences, CCG-UNAM, Mexico
 #:          https://www.ccg.unam.mx/~vinuesa/
 #           Bruno Contreras Moreira, EEAD-CSIC, Zaragoza, Spain
-#           https://digital.csic.es/cris/rp/rp02661/
+#           https://www.eead.csic.es/compbio
 #
 #: DISCLAIMER: programs of the GET_PHYLOMARKERS package are distributed in the hope that they will be useful, 
 #              but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
@@ -2517,7 +2517,7 @@ Docker images at:
 
    Alternatively, see our contact details at:
    http://www.ccg.unam.mx/~vinuesa/
-   https://digital.csic.es/cris/rp/rp02661/
+   https://www.eead.csic.es/home/staffinfo?Id=71
 
    Please run the script with the -D 1 or -D 2 added at the end of the
    command line, and send us the output, to better diagnose

run_kdetrees.R

@@ -2,9 +2,14 @@
 
 # run_kdetrees.R
 
+<<<<<<< HEAD
 VERSION <- 'Version: 0.3.1 - 20mar24'  
                  #v0.3 20Oct22 with portable shebang line
                  # runs kdetrees(all.trees.raw, distance = "dissimilarity", topo.only = TRUE &  topo.only = FALSE)
+=======
+VERSION <- 'Version: 0.3 - 20Oct2022'  #v0.3 with portable shebang line
+                                      # runs kdetrees(all.trees.raw, distance = "dissimilarity", topo.only = TRUE &  topo.only = FALSE)
+>>>>>>> 5377b250deeeccf8373a78189135bc2979b9f33d
 AUTHOR <- "Authors: Pablo Vinuesa [CCG-UNAM], Bruno Contreras Moreira [EEAD-CSIC]; "
 REPOS <- "https://cloud.r-project.org"
 

test_get_phylomarkers.t

@@ -40,7 +40,7 @@ ok( eval{ `perl ./run_parallel_cmmds.pl` } =~ /usage/ , 'run_parallel_cmmds.pl'
 ok( eval{ `Rscript ./compute_suppValStas_and_RF-dist.R 2>&1` } =~ /Usage/ , 'compute_suppValStas_and_RF-dist.R' ); 
 
 # test 11
-ok( eval{ `Rscript ./run_kdetrees.R 2>&1` } =~ /Execution/ , 'run_kdetrees.R' );
+ok( eval{ `Rscript ./run_kdetrees.R 2>&1` } =~ /Usage/ , 'run_kdetrees.R' );
 
 
 ### Test Bash scripts
@@ -84,7 +84,13 @@ ok( eval{  `cd test_sequences/core_genome && ../../run_get_phylomarkers_pipeline
 ok( eval{ `cd test_sequences/core_genome && ../../run_get_phylomarkers_pipeline.sh -R 2 -t DNA -S K2P  | grep "Will run descriptive DNA polymorphism statistics"` }, 'run_get_phylomarkers_pipeline.sh -R 2 -t DNA -S K2P' );
 
 # test 22 estimate a ML pan-genome tree from the pan-genome matrix, using 2 independent IQT runs and UFBoot
-ok( eval{ `cd test_sequences/pan_genome && ../../estimate_pangenome_phylogenies.sh -f pangenome_matrix_t0.fasta -r 2 -S UFBoot -I 2 | grep "done!"` }, 'estimate_pangenome_phylogenies.sh -r 2 -S UFBoot ...' );
+my $testOK = ok( eval{ `cd test_sequences/pan_genome && ../../estimate_pangenome_phylogenies.sh -f pangenome_matrix_t0.fasta -r 2 -S UFBoot -I 2 | grep "done!"` }, 'estimate_pangenome_phylogenies.sh -r 2 -S UFBoot ...' );
+
+if(!$testOK) {
+  print "\n# Note: this test requires setting up libnw.so . Type the following:\n\n"; 
+  print "sudo cp /PATH/TO/get_phylomarkers/lib/libnw.so /usr/local/lib && sudo echo \"export LD_LIBRARY_PATH=/usr/local/lib\" && sudo ldconfig && make clean'\n\n";
+  print "# Read more at https://github.com/eead-csic-compbio/get_phylomarkers/blob/master/INSTALL.md\n\n";
+}
 
 # test 23 estimate a PARS  pan-genome tree with bootstrapping; 50 bootstrap replicates divided on 10 core (5 reps / core)
 ok( eval{ `cd test_sequences/pan_genome && ../../estimate_pangenome_phylogenies.sh -c PARS -R 3 -i pangenome_matrix_t0.phylip -b 5 -j 1 -t 1 | grep "seq_key"` }, 'estimate_pangenome_phylogenies.sh -c PARS -R 3 ...' );