update dependencies and install process

Dockerfile

@@ -105,11 +105,11 @@ COPY .           /opt/gitrepo/container/
 RUN echo ''  ;\
     echo '==================================================================' ;\
     cd    /opt/gitrepo/container/   ;\
-    /opt/gitrepo/container/install_dependencies.sh  | tee /opt/gitrepo/container/install-dependencies.OUT.TXT  ;\
+    bash /opt/gitrepo/container/install_dependencies.sh 2>&1 | tee /opt/gitrepo/container/install-dependencies.OUT.TXT  ;\
     #git  checkout jgrg ;\   # the github workflow is doing branch specific build, so no need to do this checkout step
     git   branch | tee /opt/gitrepo/container/git.branch.OUT.TXT  ;\
     git   log --oneline --graph --decorate | tee /opt/gitrepo/container/git.lol.OUT.TXT  ;\
-    /opt/gitrepo/container/bin/abricate --setupdb  | tee /opt/gitrepo/container/abricate--setupdb.OUT.TXT  ;\
+    /opt/gitrepo/container/bin/abricate --setupdb 2>&1 | tee /opt/gitrepo/container/abricate--setupdb.OUT.TXT  ;\
     cd    /   ;\
     echo  ""
 

install_dependencies.sh

@@ -3,12 +3,21 @@
 ## install dependencies needed by abricate per
 ## https://github.com/tseemann/abricate?tab=readme-ov-file#installation
 
-sudo apt-get install bioperl ncbi-blast+ gzip unzip git \
+apt-get -y install bioperl ncbi-blast+ gzip unzip git \
   libjson-perl libtext-csv-perl libpath-tiny-perl liblwp-protocol-https-perl libwww-perl
 
+cd /opt/gitrepo
+git clone https://github.com/tseemann/any2fasta.git
+cp -p /opt/gitrepo/any2fasta/any2fasta /usr/local/bin
+which any2fasta
+
+
+cd    /opt/gitrepo/container
+cp -p /opt/gitrepo/container/bin/abricate /usr/local/bin
 ## git clone https://github.com/tseemann/abricate.git
-alias Abricate=/opt/gitrepo/container/bin/abricate
-Abricate/bin/abricate --check
-Abricate/bin/abricate --setupdb
-Abricate/bin/abricate ./abricate/test/assembly.fa
+which abricate
+abricate --check
+abricate --setupdb
+abricate ./abricate/test/assembly.fa
 
+abricate --list