First commit. WARNING: this is being added at this time to assist in a bug report, and should be considered non-functional.

3 files changed, 169 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..ca0130282ceb
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,76 @@
+pkgbase = pfam
+	pkgdesc = The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
+	pkgver = 31.0
+	pkgrel = 1
+	url = ftp://ftp.ebi.ac.uk
+	arch = any
+	license = CC0
+	makedepends = bash
+	depends = hmmer
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.dead.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.fasta.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.metagenomics.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.ncbi.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.uniprot.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.regions.tsv.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.regions.uniprot.tsv.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.rp15.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.rp35.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.rp55.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.rp75.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.seed.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-C.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam.version.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/active_site.dat.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/diff.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/metaseq.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/ncbi.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/pdbmap.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/pfamseq.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/relnotes.txt
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/swisspfam.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/trees.tgz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/uniprot.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/uniprot_reference_proteomes.dat.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/uniprot_sprot.dat.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/uniprot_trembl.dat.gz
+	source = ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/userman.txt
+	md5sums = 8951c2a33e7f77c562473097d6ac2b33
+	md5sums = 84911a0062127ed317c78cbc914ddf87
+	md5sums = 118fe71332b219fcd0a3e637f1071daa
+	md5sums = 18e8e092530bd5bea65027eafd48071d
+	md5sums = 2aefa6868e6b90e81ee3bc49f5f488d3
+	md5sums = 07addfd349bd1210d669a0943c9d4710
+	md5sums = 57b776bf6af21ad2444dc22cc0b5f52b
+	md5sums = ebd972c5d7723213b254b44362fd7ff1
+	md5sums = b6fda5fdc90d24fbc1484d3b641d4e32
+	md5sums = 05545e623b17c445e9f4daf35de299a3
+	md5sums = f5a35b1a69cbaf0ea711ab34567a5cbc
+	md5sums = 18cf5026bf9c582330bb79dc81369fbf
+	md5sums = 1ae926383d04bb8bb49c2638742ea692
+	md5sums = 55aeeab2ea19da2c80d70e10c7d24e0f
+	md5sums = 0b23fa218d00ddcb1905a5c96bb90e98
+	md5sums = 769f26046f6cd40e3b98aab20444ad07
+	md5sums = f1dd39486bbbd6ec58a4375e5792ebe7
+	md5sums = 3e47eec766a99b599cb24f28c4d393f8
+	md5sums = e3abb05823817e0c7ef77888a5c6906d
+	md5sums = 1fb93cc2ef9302cb3a77586d7a2cb31c
+	md5sums = b2d5702cd3d8cfbd91818a0eebf3230d
+	md5sums = 3db585e9bbd6b7f8a2dc97c1ff3b14b0
+	md5sums = c255691cd9e8315d7895109cc2e27de7
+	md5sums = a7361044f6e85355cb75bc2c898cc8c4
+	md5sums = d763ba0cadbc8d112ea8b160b4d684b2
+	md5sums = cda141456671a58bb320301c0d7e57d8
+	md5sums = 6421632157ebe5c596ff7b03fa4a7c38
+	md5sums = d4aa02ea20995d12ef476e5190f5640d
+	md5sums = 762a2f475b80a70114a9dffe631842bb
+	md5sums = 8595d709244198798facb83edffb0ee8
+	md5sums = c6d85f03c6b7828bc2c9cef7f77fdffd
+	md5sums = 6b5708e27461b2e705a73898be881d5f
+
+pkgname = pfam
+
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 000000000000..024cfd88bb8a
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+*.gz
+*.tgz
+*.xz
+pkg/
+relnotes.txt
+userman.txt
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..208a31cdd5b3
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,87 @@
+# Maintainer: Josh Marshall <jrmarsha@mtu.edu>
+
+pkgname=pfam
+pkgver=31.0
+pkgrel=1
+pkgdesc='The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). '
+arch=('any')
+license=('CC0')
+url='ftp://ftp.ebi.ac.uk'
+depends=('hmmer')
+makedepends=('bash')
+provides=()
+path="/pub/databases/Pfam/current_release"
+source=(
+        "$url$path/Pfam-A.clans.tsv.gz"
+        "$url$path/Pfam-A.dead.gz"
+        "$url$path/Pfam-A.fasta.gz"
+        "$url$path/Pfam-A.full.gz"
+        "$url$path/Pfam-A.full.metagenomics.gz"
+        "$url$path/Pfam-A.full.ncbi.gz"
+        "$url$path/Pfam-A.full.uniprot.gz"
+        "$url$path/Pfam-A.hmm.dat.gz"
+        "$url$path/Pfam-A.hmm.gz"
+        "$url$path/Pfam-A.regions.tsv.gz"
+        "$url$path/Pfam-A.regions.uniprot.tsv.gz"
+        "$url$path/Pfam-A.rp15.gz"
+        "$url$path/Pfam-A.rp35.gz"
+        "$url$path/Pfam-A.rp55.gz"
+        "$url$path/Pfam-A.rp75.gz"
+        "$url$path/Pfam-A.seed.gz"
+        "$url$path/Pfam-C.gz"
+        "$url$path/Pfam.version.gz"
+        "$url$path/active_site.dat.gz"
+        "$url$path/diff.gz"
+        "$url$path/metaseq.gz"
+        "$url$path/ncbi.gz"
+        "$url$path/pdbmap.gz"
+        "$url$path/pfamseq.gz"
+        "$url$path/relnotes.txt"
+        "$url$path/swisspfam.gz"
+        "$url$path/trees.tgz"
+        "$url$path/uniprot.gz"
+        "$url$path/uniprot_reference_proteomes.dat.gz"
+        "$url$path/uniprot_sprot.dat.gz"
+        "$url$path/uniprot_trembl.dat.gz"
+        "$url$path/userman.txt"
+        )
+md5sums=(
+'8951c2a33e7f77c562473097d6ac2b33'  #Pfam-A.clans.tsv.gz
+'84911a0062127ed317c78cbc914ddf87'  #Pfam-A.dead.gz
+'118fe71332b219fcd0a3e637f1071daa'  #Pfam-A.fasta.gz
+'18e8e092530bd5bea65027eafd48071d'  #Pfam-A.full.gz
+'2aefa6868e6b90e81ee3bc49f5f488d3'  #Pfam-A.full.metagenomics.gz
+'07addfd349bd1210d669a0943c9d4710'  #Pfam-A.full.ncbi.gz
+'57b776bf6af21ad2444dc22cc0b5f52b'  #Pfam-A.full.uniprot.gz
+'ebd972c5d7723213b254b44362fd7ff1'  #Pfam-A.hmm.dat.gz
+'b6fda5fdc90d24fbc1484d3b641d4e32'  #Pfam-A.hmm.gz
+'05545e623b17c445e9f4daf35de299a3'  #Pfam-A.regions.tsv.gz
+'f5a35b1a69cbaf0ea711ab34567a5cbc'  #Pfam-A.regions.uniprot.tsv.gz
+'18cf5026bf9c582330bb79dc81369fbf'  #Pfam-A.rp15.gz
+'1ae926383d04bb8bb49c2638742ea692'  #Pfam-A.rp35.gz
+'55aeeab2ea19da2c80d70e10c7d24e0f'  #Pfam-A.rp55.gz
+'0b23fa218d00ddcb1905a5c96bb90e98'  #Pfam-A.rp75.gz
+'769f26046f6cd40e3b98aab20444ad07'  #Pfam-A.seed.gz
+'f1dd39486bbbd6ec58a4375e5792ebe7'  #Pfam-C.gz
+'3e47eec766a99b599cb24f28c4d393f8'  #Pfam.version.gz
+'e3abb05823817e0c7ef77888a5c6906d'  #active_site.dat.gz
+'1fb93cc2ef9302cb3a77586d7a2cb31c'  #diff.gz
+'b2d5702cd3d8cfbd91818a0eebf3230d'  #metaseq.gz
+'3db585e9bbd6b7f8a2dc97c1ff3b14b0'  #ncbi.gz
+'c255691cd9e8315d7895109cc2e27de7'  #pdbmap.gz
+'a7361044f6e85355cb75bc2c898cc8c4'  #pfamseq.gz
+'d763ba0cadbc8d112ea8b160b4d684b2'  #relnotes.txt
+'cda141456671a58bb320301c0d7e57d8'  #swisspfam.gz
+'6421632157ebe5c596ff7b03fa4a7c38'  #trees.tgz
+'d4aa02ea20995d12ef476e5190f5640d'  #uniprot.gz
+'762a2f475b80a70114a9dffe631842bb'  #uniprot_reference_proteomes.dat.gz
+'8595d709244198798facb83edffb0ee8'  #uniprot_sprot.dat.gz
+'c6d85f03c6b7828bc2c9cef7f77fdffd'  #uniprot_trembl.dat.gz
+'6b5708e27461b2e705a73898be881d5f'  #userman.txt
+)
+
+package() {
+  mkdir -p  "$pkgdir/opt/$pkgname/"
+  rm -f *.gz *.tgz
+  find * -maxdepth 0 -regex '.+\.gz|.+\.tgz' -prune -o -print0 | xargs -0 -i mv {} "$pkgdir/opt/$pkgname/"
+}