Removed fasta36/fastx/Jalview/smart run ability, as these programs wi…

…ll no longer be supported

ChangeLog

@@ -6,7 +6,7 @@ Version 18
 	4) Removed old documentation functionality. HTML/PDF manuals are now stored in gh-pages branch and exported directly from word docs.
 	5) Changed application script jar paths.
 	6) Rewrote writedb_entry script.
-	7) Fixed broken Amigo GO term URL, used in the Artemis gene builder window.
+	7) Fixed broken Amigo, GO term, Uniprot and UniprotKB URLs, used in the Artemis gene builder/feature edit windows.
 	8) Updated README.md
 	9) Fix for RT ticket #400288: "GO term warnings in Artemis" - we now no longer put out a warning for ISM, as it's optional in certain cases
 	    [http://wiki.geneontology.org/index.php/Inferred_from_Sequence_Model_(ISM)].
@@ -16,7 +16,7 @@ Version 18
 	13) Added temporary Java 9+ --add-opens flags to art/act scripts. These will be removed when Ibatis is replaced.
 	14) Added basic unit tests for Chado access to enable Postgres 10 testing.
 	15) Added Mockito for unit test mocking.
-	16) Updated/fixed run_blast<..> and run_fast<..> scripts in the etc folder. These now use blast+. And added local blast+/fasta/fastx capability back into the Mac release.
+	16) Updated/fixed run_blast<..> scripts in the etc folder. These now use blast+. Removed options to run Smart, Jalview, fasta & fastx.
 	    Results are displayed using View->Search Results.
 	17) Removed the old icons/Readme doc for local blast setup and added an updated version to the main README.md.
 	18) Updated setup_blast_dbs.sh script and added to etc folder, for setup of local blast environment (See README.md).

README.md

@@ -75,6 +75,26 @@ Note that if you are running a build from behind a proxy you will need to add th
 ```
 mvn -Dhttps.proxyHost=myproxyhost -Dhttps.proxyPort=myproxyport -DproxySet=true package
 ```
+This will build the application jars and place them in target/jars and win-jars folders. The win-jars jars have the etc folder files bundled in, for Windows.
+
+## Building Release artifacts
+To build .zip or .gz installables with unsigned jars, use the following command:
+```
+mvn -Djarsigner.skip=true clean package -P release
+```
+If building on a Mac then .app packages and a .dmg image can additionally be produced using:
+```
+mvn -Djarsigner.skip=true clean package verify -P release
+```
+The release artifacts can then be found in the target/release-artifacts directory.
+
+Jar signing can be included in the build cycle by <b>not</b> supplying a -Djarsigner.skip flag. A <i>maven.properties</i> file needs to be placed in the top-level Artemis folder containing the following keystore properties:
+```
+signer-keystore-path=<The path to a .jks keystore>
+signer-keystore-alias=<certificate alias name>
+signer-keystore-password=<keystore password>
+signer-keystore-type=JKS
+```
 
 ## Searching and Using Local Sequence Databases
 
@@ -101,46 +121,21 @@ If you wish to do this then carry out the following steps:
   ```
   For a Mac OS X install you can mount the resulting .dmg image by double-clicking it and then selecting the .pkg installer file to actually install the BLAST+ executables into the default location (/usr/local/ncbi/blast). Comprehensive installation instructions for all operating systems are provided  [here](https://www.ncbi.nlm.nih.gov/books/NBK279690/).
 
-2. To download and install Fasta locally, check here:
-
-  ```
-  ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/
-  ```
-
-  and download the latest release, e.g.
-
-  ```
-  ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/fasta3/fasta-36.3.8g.tar.gz
-  ```
-  Uncompress the tar:
-
-  ```
-  tar -zxvf fasta-36.3.8g.tar.gz
-  ```
-
-  Build the executables, e.g. for a Mac:
-
-  ```
-  cd fasta/src
-  make -f ../make/Makefile.os_x86_64 all
-  ```
-  Move the fasta folder to a convenient area, preferably /usr/local/ for Macs:
-
-3. Ensure that the BLAST+ and Fasta executables are available in your PATH and that local databases can be found by Artemis:
+2. Ensure that the BLAST+ executables are available in your PATH and that local
+   databases can be found by Artemis:
 
   On the command line type:
 
   ```
   blastp -help
-  fasta36 -help
   ```
-  If the executables are not found then their respective installation bin folders will need to be added to your .profile PATH variable. This can be achieved by uncommenting and setting the relevant environment variables in the **Variables for locally installed Blast databases** section of the Artemis **setenv** script. The location of the databases is assumed by default to be &lt;home directory&gt;/blast-data but this can be overridden by setting the BLASTDB and FASTLIBS variables. The setenv script should then be called from your login **.profile** file. Alternatively copy the relevant variables into your profile.
+  If the executables are not found then their respective installation bin folders will need to be added to your .profile PATH variable. This can be achieved by uncommenting and setting the relevant environment variables in the **Variables for locally installed Blast databases** section of the Artemis **setenv** script. The location of the databases is assumed by default to be &lt;home directory&gt;/blast-data but this can be overridden by setting the BLASTDB variable (See Blast+ documentation). The setenv script should then be called from your login **.profile** file. Alternatively copy the relevant variables into your profile.
 
   Note that database locations can also be specified directly within the Artemis/ACT applications.
 
 4. Download and format the uniprot database(s):
 
-  You can do this by using the Artemis etc/setup_uniprot_dbs.sh script. This script can be changed as desired, to for instance, include additional databases or create a FASTLIBS file.
+  You can do this by using the Artemis etc/setup_uniprot_dbs.sh script. This script can be changed as desired, to for instance, include additional databases.
 
   ```
   mkdir $HOME/blast-data

etc/options

@@ -767,35 +767,24 @@ invisible_qualifiers_gff= \
 # search.
 #
 feature_protein_programs = \
-    fasta %uniprot \
-    fasta %uniprot_archaea \
-    fasta %uniprot_bacteria \
-    fasta %uniprot_eukaryota \
-    fasta %uniprot_viruses \
-    fasta %uniprot_rest \
-    fasta %malaria \
-    sigcleave 0 \
-    pepstats - \
     blastp uniprot \
     blastp uniprot_archaea \
     blastp uniprot_bacteria \
     blastp uniprot_eukaryota \
     blastp uniprot_viruses \
     tblastn %embl_other \
     hth - \
-    smart - \
-    clustalx PROTEIN \
-    jalview PROTEIN
+    sigcleave 0 \
+    pepstats - \
+    clustalx PROTEIN
 
 feature_dna_programs = \
     tblastx %embl_other \
     blastn %embl_other \
     blastx %uniprot \
-    fastx %uniprot \
     clustalx DNA
 
-application_programs = \
-    jalview
+application_programs =
 
 ncbi_dna_search = \
    blastn http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&MEGABLAST=on&BLAST_PROGRAMS=blastn&PAGE_TYPE=BlastSearch&DATABASE=nr&SHOW_DEFAULTS=on&QUERY= \
@@ -818,12 +807,11 @@ common_keys = \
     BLASTN_HIT BLASTCDS 3'UTR 5'UTR
 
 # SRS
-#srs_url = http://srs.ebi.ac.uk/srsbin/cgi-bin/
 srs_url = http://www.bioinformatics.nl/srsbin/cgi-bin/
 
 # hyperlinked databases in feature editor
 hyperlinks = \
-  SWALL+UniProt+UniProtKB srs_url \
+  SWALL srs_url \
   EMBL http://www.ebi.ac.uk/Tools/dbfetch/expasyfetch? \
   PubMed+PMID http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch= \
   InterPro http://www.ebi.ac.uk/interpro/entry/ \
@@ -844,6 +832,8 @@ hyperlinks = \
   GeneID http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids= \
   Rfam http://rfam.sanger.ac.uk/family/ \
   GI http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi?val= \
+  UniProt https://www.uniprot.org/uniprot/ \
+  UniProtKB https://www.uniprot.org/uniprot/ \
   TCDB http://www.tcdb.org/search/result.php?tc=
 
 # BamView