From 3bb059b3c7aac888129f81355fefc59c0db2f1db Mon Sep 17 00:00:00 2001 From: kullrich Date: Fri, 22 Dec 2023 08:17:26 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20kullrich?= =?UTF-8?q?/CRBHits@2f12c74c2b1287b6a47cabd324774d0a53dd207b=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/V01CRBHitsBasicVignette.html | 6 +++--- articles/V02KaKsVignette.html | 4 ++-- index.html | 18 +++++++++--------- pkgdown.yml | 2 +- reference/aa2rbh.html | 6 +++--- reference/aafile2rbh.html | 6 +++--- reference/cds2kaks.html | 5 ++++- reference/cds2rbh.html | 6 +++--- reference/cdsdir2orthofinder.html | 6 +++--- reference/cdsfile2rbh.html | 6 +++--- reference/make_last.html | 4 ++-- reference/make_vignette.html | 4 ++-- reference/rbh2dagchainer.html | 2 +- reference/rbh2kaks.html | 2 +- 14 files changed, 40 insertions(+), 37 deletions(-) diff --git a/articles/V01CRBHitsBasicVignette.html b/articles/V01CRBHitsBasicVignette.html index 324764a..564e4fc 100644 --- a/articles/V01CRBHitsBasicVignette.html +++ b/articles/V01CRBHitsBasicVignette.html @@ -89,7 +89,7 @@

CRBHits Basic Vignette

Kristian K Ullrich

-

2023-05-19

+

2023-12-22

Source: vignettes/V01CRBHitsBasicVignette.Rmd @@ -186,7 +186,7 @@

Table of Contentsmake_last(), make_KaKs_Calculator2() and make_dagchainer() you won’t need to specify the paths anymore. Please remove them if you @@ -227,7 +227,7 @@

1. InstallationFor the windows platform the user needs to use e.g. https://www.cygwin.com/ to be able to compile the prerequisites.

library(CRBHits)
-## compile last-1453
+## compile last-1521
 make_last()
 ## compile KaKs_Calculator2.0
 make_KaKs_Calculator2()
diff --git a/articles/V02KaKsVignette.html b/articles/V02KaKsVignette.html
index e5fe9d0..7e17c2f 100644
--- a/articles/V02KaKsVignette.html
+++ b/articles/V02KaKsVignette.html
@@ -89,7 +89,7 @@ 
KaKs Vignette

                         
Kristian K
 Ullrich

             
-            
2023-05-19

+            
2023-12-22

       
       Source: vignettes/V02KaKsVignette.Rmd
       
@@ -176,7 +176,7 @@ 
Table of Contentsmake_last(),
 make_KaKs_Calculator2() and make_dagchainer()
 you won’t need to specify the paths anymore. Please remove them if you
diff --git a/index.html b/index.html
index bdcbdd0..eb1d55a 100644
--- a/index.html
+++ b/index.html
@@ -190,7 +190,7 @@ 
Quick-guidelibrary(CRBHits)
 ## prerequisite: last
-## if not done yet, try to compile last-1453 - uncomment the following line
+## if not done yet, try to compile last-1521 - uncomment the following line
 #CRBHits::make_last()
 ## conditional reciprocal best hits (CRBHit pairs)
 data("ath", package="CRBHits")
@@ -277,7 +277,7 @@ 
Quick-guide##### see section compile external tools from original source code
 ## example how to use own compiled version of LAST
-my.lastpath <- "/tmp/last/last-1453/bin"
+my.lastpath <- "/tmp/last/last-1521/bin"
 ath_aly_crbh <- cds2rbh(ath, aly, plotCurve = TRUE,
                         lastpath = my.lastpath)
 ?cds2rbh
@@ -337,7 +337,7 @@ 
comp
 
The source code for the prerequisites (LAST, KaKs_Calculator2.0, DAGchainer) are forked within CRBHits.

 
 
To compile the forked version of LAST within the CRBHits R package directory try to use the function make_last():

@@ -366,10 +366,10 @@ 
compile external tools
 ## e.g.
 mkdir /tmp/last
 cd /tmp/last
-## donwload last-1453
-curl -O https://gitlab.com/mcfrith/last/-/archive/1453/last-1453.zip
-unzip last-1453.zip
-cd last-1453
+## donwload last-1521
+curl -O https://gitlab.com/mcfrith/last/-/archive/1521/last-1521.zip
+unzip last-1521.zip
+cd last-1521
 ## compile LAST
 make

To compile KaKs_Calculator2.0:

@@ -399,7 +399,7 @@

compile external tools make

If you would like to use your own compiled versions of LAST, KaKs_Calculator2.0 and DAGchainer you need to set the correct @param in the corresponding functions of CRBHits.

## example how to use own compiled versions of LAST, KaKs_Calculator2.0 and DAGchainer
-my.lastpath <- "/tmp/last/last-1453/bin"
+my.lastpath <- "/tmp/last/last-1521/bin"
 my.kakspath <- "/tmp/KaKs_Calculator2/KaKs_Calculator2.0_src/src"
 my.dagchainerpath <- "/tmp/dagcahiner"
 
@@ -421,7 +421,7 @@ 
LicenseMIT (see LICENSE)

 
The CRBHits package includes source code that has been published under following licenses:

 

-
last-1453.zip
+
last-1521.zip
 

 
GNU General Public License Version 3, 29 June 2007 GPLv3

 

diff --git a/pkgdown.yml b/pkgdown.yml
index 3a9c9c5..765ee75 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   V01CRBHitsBasicVignette: V01CRBHitsBasicVignette.html
   V02KaKsVignette: V02KaKsVignette.html
-last_built: 2023-05-19T11:29Z
+last_built: 2023-12-22T08:14Z
 
diff --git a/reference/aa2rbh.html b/reference/aa2rbh.html
index 98bdf36..6bfaa60 100644
--- a/reference/aa2rbh.html
+++ b/reference/aa2rbh.html
@@ -87,7 +87,7 @@ 
aa2rbh

   aa1,
   aa2,
   searchtool = "last",
-  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1453/bin/"),
+  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1521/bin/"),
   lastD = 1e+06,
   mmseqs2path = NULL,
   mmseqs2sensitivity = 5.7,
@@ -130,7 +130,7 @@ 
Arguments

 
 
lastpath

 
specify the PATH to the last binaries
-[default: /extdata/last-1453/bin/]

+[default: /extdata/last-1521/bin/]

 
 
 
lastD

@@ -290,7 +290,7 @@ 
Author

 
     

     
Examples

-    
## compile last-1453 within CRBHits
+    
## compile last-1521 within CRBHits
 CRBHits::make_last()
 ## load example sequence data
 data("ath", package="CRBHits")
diff --git a/reference/aafile2rbh.html b/reference/aafile2rbh.html
index 7bc6519..74fb48c 100644
--- a/reference/aafile2rbh.html
+++ b/reference/aafile2rbh.html
@@ -89,7 +89,7 @@ 
aafile2rbh

   aafile1,
   aafile2,
   searchtool = "last",
-  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1453/bin/"),
+  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1521/bin/"),
   lastD = 1e+06,
   mmseqs2path = NULL,
   mmseqs2sensitivity = 5.7,
@@ -132,7 +132,7 @@ 
Arguments

 
 
lastpath

 
specify the PATH to the last binaries
-[default: /extdata/last-1453/bin/]

+[default: /extdata/last-1521/bin/]

 
 
 
lastD

@@ -292,7 +292,7 @@ 
Author

 
     

     
Examples

-    
## compile last-1453 within CRBHits
+    
## compile last-1521 within CRBHits
 CRBHits::make_last()
 ## load example sequence data
 athfile <- system.file("fasta", "ath.aa.fasta.gz", package="CRBHits")
diff --git a/reference/cds2kaks.html b/reference/cds2kaks.html
index ea4a16d..029a184 100644
--- a/reference/cds2kaks.html
+++ b/reference/cds2kaks.html
@@ -91,7 +91,10 @@ 
Arguments

 
 
 
model

-
specify codon model either "Li" or "YN" or "NG86" [default: Li]

+
specify codon model either "Li" or "NG86"
+or one of KaKs_Calculator2 model "NG", "LWL", "LPB", "MLWL",
+"MLPB", "GY", "YN", "MYN", "MS", "MA", "GNG", "GLWL", "GLPB",
+"GMLWL", "GMLPB", "GYN", "GMYN" [default: Li]

 
 
 
kakscalcpath

diff --git a/reference/cds2rbh.html b/reference/cds2rbh.html
index 8fd88bd..a31b2b2 100644
--- a/reference/cds2rbh.html
+++ b/reference/cds2rbh.html
@@ -85,7 +85,7 @@ 
cds2rbh

   cds1,
   cds2,
   searchtool = "last",
-  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1453/bin/"),
+  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1521/bin/"),
   lastD = 1e+06,
   mmseqs2path = NULL,
   mmseqs2sensitivity = 5.7,
@@ -138,7 +138,7 @@ 
Arguments

 
 
lastpath

 
specify the PATH to the last binaries
-[default: /extdata/last-1453/bin/]

+[default: /extdata/last-1521/bin/]

 
 
 
lastD

@@ -345,7 +345,7 @@ 
Author

 
     

     
Examples

-    
## compile last-1453 within CRBHits
+    
## compile last-1521 within CRBHits
 CRBHits::make_last()
 ## load example sequence data
 data("ath", package="CRBHits")
diff --git a/reference/cdsdir2orthofinder.html b/reference/cdsdir2orthofinder.html
index 5a079d7..3ffd919 100644
--- a/reference/cdsdir2orthofinder.html
+++ b/reference/cdsdir2orthofinder.html
@@ -83,7 +83,7 @@ 
cdsdir2orthofinder

   dir,
   file_ending = "*",
   searchtool = "last",
-  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1453/bin/"),
+  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1521/bin/"),
   lastD = 1e+06,
   mmseqs2path = NULL,
   mmseqs2sensitivity = 5.7,
@@ -124,7 +124,7 @@ 
Arguments

 
 
lastpath

 
specify the PATH to the last binaries
-[default: /extdata/last-1453/bin/]

+[default: /extdata/last-1521/bin/]

 
 
 
lastD

@@ -249,7 +249,7 @@ 
Author

 
     

     
Examples

-    
## compile last-1453 within CRBHits
+    
## compile last-1521 within CRBHits
 CRBHits::make_last()
 

     

diff --git a/reference/cdsfile2rbh.html b/reference/cdsfile2rbh.html
index 1a87e6f..6d70535 100644
--- a/reference/cdsfile2rbh.html
+++ b/reference/cdsfile2rbh.html
@@ -87,7 +87,7 @@ 
cdsfile2rbh

   cdsfile1,
   cdsfile2,
   searchtool = "last",
-  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1453/bin/"),
+  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1521/bin/"),
   lastD = 1e+06,
   mmseqs2path = NULL,
   mmseqs2sensitivity = 5.7,
@@ -140,7 +140,7 @@ 
Arguments

 
 
lastpath

 
specify the PATH to the last binaries
-[default: /extdata/last-1453/bin/]

+[default: /extdata/last-1521/bin/]

 
 
 
lastD

@@ -349,7 +349,7 @@ 
Author

 
     

     
Examples

-    
## compile last-1453 within CRBHits
+    
## compile last-1521 within CRBHits
 CRBHits::make_last()
 ## load example sequence data
 athfile <- system.file("fasta", "ath.cds.fasta.gz", package="CRBHits")
diff --git a/reference/make_last.html b/reference/make_last.html
index 21c4c93..d7c7a7e 100644
--- a/reference/make_last.html
+++ b/reference/make_last.html
@@ -1,5 +1,5 @@
 
-make_last — make_last • CRBHitsmake_last — make_last • CRBHitsmake_vignette — make_vignette • CRBHitsmake_vignette — make_vignette • CRBHits