1.87

CHANGELOG.md

@@ -3,12 +3,15 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## 1.87 - 2023-10/17
+### Updated
+- genometools: `1.6.0` -> `1.6.4`
+- coseg: `0.2.2` -> `0.2.3`
+
 ## 1.86 - 2023-10/09
 ### Updated
 - RMBlast: `2.14.0` -> `2.14.1`
 - RepeatModeler: `2.0.4` -> `2.0.5`
-- genometools: `1.6.0` -> `1.6.4`
-- coseg: `0.2.2` -> `0.2.3`
 
 ## 1.85 - 2023-5/09
 ### Updated

Dockerfile

@@ -22,7 +22,6 @@ RUN apt-get -y update && apt-get -y install \
 
 COPY src/* /opt/src/
 COPY sha256sums.txt /opt/src/
-COPY container_test.sh /opt/src/
 WORKDIR /opt/src
 
 RUN sha256sum -c sha256sums.txt
@@ -147,4 +146,6 @@ ENV LANG=C
 ENV PYTHONIOENCODING=utf8
 ENV PATH=/opt/RepeatMasker:/opt/RepeatMasker/util:/opt/RepeatModeler:/opt/RepeatModeler/util:/opt/coseg:/opt/ucsc_tools:/opt:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/opt/rmblast/bin:/bin
 
+COPY container_test.sh /opt/src/
+RUN chmod 701 /opt/src/container_test.sh
 RUN /opt/src/container_test.sh

README.md

@@ -161,7 +161,7 @@ singularity build dfam-tetools.sif dfam-tetools.def
 
 ## Included software
 
-The following software is included in the Dfam TE Tools container (version `1.86`):
+The following software is included in the Dfam TE Tools container (version `1.87`):
 
 | | | |
 | -------------- | -------- | --- |

container_test.sh

@@ -1,10 +1,61 @@
-#!/bin/sh
+#!/bin/bash
 
-set -eu
-
-declare -A tests=(
-    ["rmblast"]='/opt/rmblast/bin/rmblast -help'
-    ["other"]='placeholder'
+declare -A installation_tests=(
+    ["rmblast"]='/opt/rmblast/bin/rmblastn'
+    ["hmmr"]='/opt/hmmer/bin/nhmmer' 
+    ["trf"]='/opt/trf'
+    ["repeat_scout"]='/opt/RepeatScout/RepeatScout'
+    ["recon"]='/opt/RECON/bin/famdef'
+    ["cd-hit"]='/opt/cd-hit/cd-hit'
+    ["genometools"]='/opt/genometools/bin/gt'
+    ["mafft"]='/opt/mafft/libexec/mafft/mafft-distance'
+    ["ninja"]='/opt/NINJA/NINJA/Ninja'
+    ["faToTwoBit"]='/opt/ucsc_tools/faToTwoBit'
+    ["twoBitInfo"]='/opt/ucsc_tools/twoBitInfo'
+    ["twoBitToFa"]='/opt/ucsc_tools/twoBitToFa'
+    ["coseg"]='/opt/coseg/coseg'
 )
-echo "${tests[other]}"
-for test in "${!tests[@]}"; do echo "$test - ${tests[$test]}"; done
+
+run_installation_test () {
+    test="$1"
+    if ldd "${installation_tests[$test]}" | grep -q 'not found'
+    then
+        echo " - $test ERROR"
+    else
+        echo " - $test is installed correctly"
+    fi
+}
+
+echo 'Running Installation Tests'
+for test in "${!installation_tests[@]}"; do run_installation_test $test; done
+
+# TODO - test outputs of installed programs
+# declare -A functional_tests=(
+#     ["rmblast"]='placeholder'
+#     ["hmmr"]='placeholder' 
+#     ["trf"]='placeholder'
+#     ["repeat_scout"]='placeholder'
+#     ["recon"]='placeholder'
+#     ["cd-hit"]='placeholder'
+#     ["genometools"]='placeholder'
+#     ["ltr_retriever"]='placeholder'
+#     ["mafft"]='placeholder'
+#     ["ninja"]='placeholder'
+#     ["faToTwoBit"]='placeholder'
+#     ["twoBitInfo"]='placeholder'
+#     ["twoBitToFa"]='placeholder'
+#     ["coseg"]='placeholder'
+#     ["repeatmasker"]='placeholder'
+#     ["repeatmodeler"]='placeholder'
+# )
+# run_functional_test () {
+#     test="$1"
+#     if placeholder
+#     then
+#         echo "$test" "error"
+#     else
+#         echo "$test" "is working"
+#     fi
+# }
+# echo 'Running Functional Tests'
+# for test in "${!functional_tests[@]}"; do run_functional_test $test; done

dfam-tetools.sh

@@ -31,7 +31,7 @@ programs are available, singularity is preferred."
 
 ## Parse command-line arguments ##
 
-container="dfam/tetools:1.86"
+container="dfam/tetools:1.87"
 use_docker=0
 use_singularity=0
 

releasing.md

@@ -14,6 +14,7 @@
 3. Build the container (see `README.md`)
   * Use the tag `dfam/tetools:dev`
 4. Test the container
+  * `container_test.sh` will run as the last step of the build
 5. Commit and tag in git as x.y
   * run `git tag -a x.y`
 6. Tag the container (in docker) as `:x`, `:x.y`, and `:latest`