From 266ed6c1851b5bc7e1f800267749782b4a7cdb9b Mon Sep 17 00:00:00 2001
From: Vanessasaurus <814322+vsoch@users.noreply.github.com>
Date: Mon, 31 Oct 2022 21:04:28 -0600
Subject: [PATCH] fixing bug in workflow, emboss recipe, and derivation script
 for biocontainers (#40)

Signed-off-by: vsoch <vsoch@users.noreply.github.com>
---
 .github/scripts/update_biocontainers.py     |   6 ++
 .github/workflows/update-biocontainers.yaml |   2 +-
 quay.io/biocontainers/emboss/container.yaml | 113 +++++++++++++++++---
 3 files changed, 107 insertions(+), 14 deletions(-)

diff --git a/.github/scripts/update_biocontainers.py b/.github/scripts/update_biocontainers.py
index edfd19412e655..0d82813eaae91 100644
--- a/.github/scripts/update_biocontainers.py
+++ b/.github/scripts/update_biocontainers.py
@@ -99,6 +99,8 @@ def include_path(path):
     ]:
         if path.endswith(ending):
             return False
+    if os.path.basename(path).startswith("_"):
+        return False
     if os.path.basename(path).startswith("."):
         return False
     if "[" in path or "]" in path or "README" in path:
@@ -156,6 +158,9 @@ def main():
         keepers = {}
         for x, path in aliases.items():
 
+            if not include_path(path):
+                continue
+
             # Always use a regular expression of the image name to include
             if re.search(image_name.lower(), path.lower()):
                 keepers[x] = path
@@ -193,6 +198,7 @@ def main():
             print(f"Issue adding container {container}")
 
     # Now add those not yet seen!
+    return
     print(f"Found {len(seen)} containers already added.")
     response = requests.get("https://depot.galaxyproject.org/singularity/")
     soup = BeautifulSoup(response.text, "html.parser")
diff --git a/.github/workflows/update-biocontainers.yaml b/.github/workflows/update-biocontainers.yaml
index d5c15d62ce3c9..e00da103d985e 100644
--- a/.github/workflows/update-biocontainers.yaml
+++ b/.github/workflows/update-biocontainers.yaml
@@ -22,7 +22,7 @@ jobs:
       run: |
         git clone https://github.com/singularityhub/shpc-registry-cache /tmp/cache
         printf "python .github/scripts/update_biocontainers.py --cache /tmp/cache --registry $(pwd) --min-count-inclusion 10 --additional-count-inclusion 25\n"
-        python .github/scripts/update_biocontainers.py ---cache /tmp/cache --registry $(pwd) --min-count-inclusion 10 --additional-count-inclusion 10
+        python .github/scripts/update_biocontainers.py --cache /tmp/cache --registry $(pwd) --min-count-inclusion 10 --additional-count-inclusion 10
 
     - name: Checkout Update branch
       env:
diff --git a/quay.io/biocontainers/emboss/container.yaml b/quay.io/biocontainers/emboss/container.yaml
index 9999a82ccaa68..1461ef10116fd 100644
--- a/quay.io/biocontainers/emboss/container.yaml
+++ b/quay.io/biocontainers/emboss/container.yaml
@@ -7,21 +7,108 @@ tags:
   6.6.0--haa49230_5: sha256:51a26af4f2349bcb017855d7e797bcdb787e9177b3067ff439ccdeac550991ab
 docker: quay.io/biocontainers/emboss
 aliases:
-  _embossdata: /usr/local/bin/_embossdata
-  _embossversion: /usr/local/bin/_embossversion
-  _jembossctl: /usr/local/bin/_jembossctl
   embossdata: /usr/local/bin/embossdata
   embossupdate: /usr/local/bin/embossupdate
   embossversion: /usr/local/bin/embossversion
   jembossctl: /usr/local/bin/jembossctl
   runJemboss.sh: /usr/local/bin/runJemboss.sh
-  _bdftogd: /usr/local/bin/_bdftogd
-  _gd2copypal: /usr/local/bin/_gd2copypal
-  _gd2togif: /usr/local/bin/_gd2togif
-  _gd2topng: /usr/local/bin/_gd2topng
-  _gdcmpgif: /usr/local/bin/_gdcmpgif
-  _gdparttopng: /usr/local/bin/_gdparttopng
-  _gdtopng: /usr/local/bin/_gdtopng
-  _giftogd2: /usr/local/bin/_giftogd2
-  _pngtogd: /usr/local/bin/_pngtogd
-  _pngtogd2: /usr/local/bin/_pngtogd2
+  xmlget: /usr/local/bin/xmlget
+  xmltext: /usr/local/bin/xmltext
+  aaindexextract: /usr/local/bin/aaindexextract
+  abiview: /usr/local/bin/abiview
+  acdc: /usr/local/bin/acdc
+  acdgalaxy: /usr/local/bin/acdgalaxy
+  acdlog: /usr/local/bin/acdlog
+  acdpretty: /usr/local/bin/acdpretty
+  acdtable: /usr/local/bin/acdtable
+  acdtrace: /usr/local/bin/acdtrace
+  acdvalid: /usr/local/bin/acdvalid
+  aligncopy: /usr/local/bin/aligncopy
+  aligncopypair: /usr/local/bin/aligncopypair
+  antigenic: /usr/local/bin/antigenic
+  assemblyget: /usr/local/bin/assemblyget
+  backtranambig: /usr/local/bin/backtranambig
+  backtranseq: /usr/local/bin/backtranseq
+  banana: /usr/local/bin/banana
+  biosed: /usr/local/bin/biosed
+  btwisted: /usr/local/bin/btwisted
+  cachedas: /usr/local/bin/cachedas
+  cachedbfetch: /usr/local/bin/cachedbfetch
+  cacheebeyesearch: /usr/local/bin/cacheebeyesearch
+  cacheensembl: /usr/local/bin/cacheensembl
+  chaos: /usr/local/bin/chaos
+  charge: /usr/local/bin/charge
+  checktrans: /usr/local/bin/checktrans
+  cirdna: /usr/local/bin/cirdna
+  codcmp: /usr/local/bin/codcmp
+  codcopy: /usr/local/bin/codcopy
+  coderet: /usr/local/bin/coderet
+  compseq: /usr/local/bin/compseq
+  cons: /usr/local/bin/cons
+  consambig: /usr/local/bin/consambig
+  cpgplot: /usr/local/bin/cpgplot
+  cpgreport: /usr/local/bin/cpgreport
+  cusp: /usr/local/bin/cusp
+  cutgextract: /usr/local/bin/cutgextract
+  cutseq: /usr/local/bin/cutseq
+  dan: /usr/local/bin/dan
+  dbiblast: /usr/local/bin/dbiblast
+  dbifasta: /usr/local/bin/dbifasta
+  dbiflat: /usr/local/bin/dbiflat
+  dbigcg: /usr/local/bin/dbigcg
+  dbtell: /usr/local/bin/dbtell
+  dbxcompress: /usr/local/bin/dbxcompress
+  dbxedam: /usr/local/bin/dbxedam
+  dbxfasta: /usr/local/bin/dbxfasta
+  dbxflat: /usr/local/bin/dbxflat
+  dbxgcg: /usr/local/bin/dbxgcg
+  dbxobo: /usr/local/bin/dbxobo
+  dbxreport: /usr/local/bin/dbxreport
+  dbxresource: /usr/local/bin/dbxresource
+  dbxstat: /usr/local/bin/dbxstat
+  dbxtax: /usr/local/bin/dbxtax
+  dbxuncompress: /usr/local/bin/dbxuncompress
+  degapseq: /usr/local/bin/degapseq
+  density: /usr/local/bin/density
+  descseq: /usr/local/bin/descseq
+  diffseq: /usr/local/bin/diffseq
+  distmat: /usr/local/bin/distmat
+  dotmatcher: /usr/local/bin/dotmatcher
+  dotpath: /usr/local/bin/dotpath
+  dottup: /usr/local/bin/dottup
+  dreg: /usr/local/bin/dreg
+  drfinddata: /usr/local/bin/drfinddata
+  drfindformat: /usr/local/bin/drfindformat
+  drfindid: /usr/local/bin/drfindid
+  drfindresource: /usr/local/bin/drfindresource
+  drget: /usr/local/bin/drget
+  drtext: /usr/local/bin/drtext
+  edamdef: /usr/local/bin/edamdef
+  edamhasinput: /usr/local/bin/edamhasinput
+  edamhasoutput: /usr/local/bin/edamhasoutput
+  edamisformat: /usr/local/bin/edamisformat
+  edamisid: /usr/local/bin/edamisid
+  edamname: /usr/local/bin/edamname
+  edialign: /usr/local/bin/edialign
+  einverted: /usr/local/bin/einverted
+  emma: /usr/local/bin/emma
+  emowse: /usr/local/bin/emowse
+  entret: /usr/local/bin/entret
+  epestfind: /usr/local/bin/epestfind
+  eprimer3: /usr/local/bin/eprimer3
+  eprimer32: /usr/local/bin/eprimer32
+  equicktandem: /usr/local/bin/equicktandem
+  est2genome: /usr/local/bin/est2genome
+  etandem: /usr/local/bin/etandem
+  extractalign: /usr/local/bin/extractalign
+  extractfeat: /usr/local/bin/extractfeat
+  featcopy: /usr/local/bin/featcopy
+  featmerge: /usr/local/bin/featmerge
+  featreport: /usr/local/bin/featreport
+  feattext: /usr/local/bin/feattext
+  findkm: /usr/local/bin/findkm
+  freak: /usr/local/bin/freak
+  fuzznuc: /usr/local/bin/fuzznuc
+  fuzzpro: /usr/local/bin/fuzzpro
+  fuzztran: /usr/local/bin/fuzztran
+  garnier: /usr/local/bin/garnier