[med-svn] [pssh2] 01/08: Added skeleton for PredictProtein PSSH2
Andreas Tille
tille at debian.org
Mon Dec 18 21:13:31 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pssh2.
commit 22e37995b9f9cc7049b4b2bd6f4844a93119d824
Author: Steffen Moeller <moeller at debian.org>
Date: Sat Dec 5 14:14:07 2015 +0000
Added skeleton for PredictProtein PSSH2
---
debian/README.Debian | 16 ++++++++
debian/README.source | 37 +++++++++++++++++++
debian/changelog | 20 ++++++++++
debian/compat | 1 +
debian/control | 27 ++++++++++++++
debian/copyright | 24 ++++++++++++
debian/docs | 0
debian/manpage.1 | 101 +++++++++++++++++++++++++++++++++++++++++++++++++++
debian/pssh2.install | 15 ++++++++
debian/rules | 21 +++++++++++
10 files changed, 262 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..85e24bf
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,16 @@
+PSSH2
+=====
+
+To use this package, also download databases generated from
+PDB from
+
+ ftp://rostlab.org/pssh2/pdb_full/
+
+This package provides the script files needed to run within
+PredictProtein. Thees are all called in the correct order in
+the folder pp_pssh2. However, the tool may also be run on its
+own, i.e. independent from PredictProtein.
+
+The package expects a mysql database to provide information.
+downloadaed from above FTP server. The respective configuration
+is kept in pssh2.conf
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..bbf9f05
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,37 @@
+#!/bin/sh
+
+cat <<EOINTRO
+
+PSSH2 - changes to source code
+==============================
+
+No changes to the source get have been made, but not everything in the
+project's github folder is required for the package. The source of this
+packages was collected via this script.
+
+EOINTRO
+
+#git clone https://github.com/aschafu/PSSH2.git
+GIT=PSSH2
+DEST=pssh2-0.1
+if [ ! -d "$DEST" ]; then mkdir -p "$DEST"; fi
+
+cp -vp $GIT/src/pssh2/build_hhblits_profile "$DEST"
+cp -vp $GIT/src/pssh2/scan_structures_hhblits "$DEST"
+cp -vp $GIT/src/pssh2/fasta_to_md5 "$DEST"
+cp -vp $GIT/src/pssh2/parse_hhr_for_pssh2 "$DEST"
+cp -vp $GIT/src/pssh2/pssh2_seq "$DEST"
+cp -vp $GIT/src/pssh2/pp_pssh2 "$DEST"
+cp -vp $GIT/src/pssh2/pssh2_multi_md5 "$DEST"
+cp -vp $GIT/src/pssh2/pssh2_aws "$DEST"
+cp -vp $GIT/src/pssh2/pssh2.conf "$DEST"
+cp -vp $GIT/src/util/DB.pssh2_local "$DEST"
+cp -vp $GIT/src/util/DB.aquaria_local "$DEST"
+cp -vp $GIT/src/util/get_fasta_for_md5 "$DEST"
+cp -vp $GIT/src/util/find_cache_path "$DEST"
+cp -vp $GIT/src/pdb_full/make_new_hhblits_db "$DEST"
+cp -vp $GIT/src/pdb_full/build_hhblits_structure_profile "$DEST"
+cp -vp $GIT/src/pdb_full/find_best_pdb_for_seqres_md5 "$DEST"
+
+tar --exclude debian -cJvf pssh2_0.1.orig.tar.xz pssh2-0.1/
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f80c1d3
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,20 @@
+pssh2 (0.1) UNRELEASED; urgency=low
+
+ [ Andreas Schafferhans ]
+ * Initial release (Closes: #000)
+ * New upstream release
+ - Debugged conf_file, option passing
+ - Added multiple table query to get_fasta_for_md5, updated conf_file
+ - Reworked config file searching mechanism
+ - Added big sequence capabilities
+ - Added pssh2_aws for running on AWS
+ - Added code for creating pdb_full files
+ - Debugged conf_file further: better usage of local conf files
+ - Reworked pdb_full generation: script now generically makes hhblits databases
+
+ [ Steffen Moeller - sponsor ]
+ * still preparing getData extension for download of external data
+ * location and detection of configuration files needs to be clarified
+ * rework/rething wording in debian/control
+
+ -- Andrea Schafferhans <andrea at rostlab.org> Thu, 02 Nov 2015 13:55:16 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..fdc75e9
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,27 @@
+Source: pssh2
+Section: science
+Priority: optional
+Maintainer: Andrea Schafferhans <andrea.schafferhans at rostlab.org>
+Build-Depends: debhelper (>= 8.0.0)
+Standards-Version: 3.9.6
+Homepage: http://www.rostlab.org
+Vcs-Svn: svn://anoncvs.debian.org/collab-maint/pssh2.git
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/pssh2/trunk/
+
+Package: pssh2
+Architecture: any
+Depends: bash, perl, ruby, hhsuite
+Description: set of scripts for mapping protein sequence to structure
+ pssh2 creates sequence-to-structure alignments based on
+ hhblits profiles built for the query sequence.
+ pssh2 consists of scripts to run the hhblits queries
+ and parse the output.
+ You also need the pdb_full database downloaded from rostlab.org:
+ ftp://rostlab.org/pssh2/pdb_full/
+ .
+ This package provides the script files needed to run within
+ PredictProtein.
+ They are all called in the correct order in pp_pssh2.
+ It also contains scripts to run independent of PredictProtein.
+ It assumes you have a mysql database to store information.
+ The configuration information is kept in pssh2.conf
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..a5b10a7
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,24 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pssh2
+Source: https://aschafu@github.com/aschafu/PSSH2.git
+
+Files: *
+Copyright: 2014 Andrea Schafferhans <andrea.schafferhans at rostlab.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e69de29
diff --git a/debian/manpage.1 b/debian/manpage.1
new file mode 100644
index 0000000..8dd1d0a
--- /dev/null
+++ b/debian/manpage.1
@@ -0,0 +1,101 @@
+." Text automatically generated by txt2man
+.TH untitled "June 29, 2015" "" ""
+.SH NAME
+\fBpssh2_multi_md5 \fP- generate pssh2 type sequence-to-structrue alignments for many sequences given md5 sums
+.SH SYNOPSIS
+.nf
+.fam C
+\fBpssh2_multi_md5\fP [\fB-h\fP] [\fB-D\fP] [\fB-m\fP \"md5 \fIinput\fP list\"] [-- \.\.\.]
+.fam T
+.fi
+.SH DESCRIPTION
+\fBpssh2_multi_md5\fP takes md5 sums from the command line (behind \fB-m\fP),
+gets the associated sequences from the database,
+and runs pssh2 for each of the sequences (which adds the alignment to the database).
+See pssh2_seq \fB-h\fP for more details on pssh2_seq.
+Defaults are configured in /etc/pssh2.conf.
+.SH OPTIONS
+.TP
+.B
+\fB-h\fP
+The option \fB-h\fP displays help and exits.
+.TP
+.B
+\fB-D\fP
+Debug option: do not remove or zip output files (passed on to pssh2_seq)
+Any other parameters behind "--" are passed on to the child scripts.
+.SH AUTHOR
+Andrea Schafferhans <andrea.schafferhans at rostlab.org>
+.SH NAME
+\fBpssh2_seq \fP- generate pssh2 type sequence-to-structrue alignments
+.SH SYNOPSIS
+.nf
+.fam C
+\fBpssh2_seq\fP [\fB-s\fP] [\fB-h\fP] [\fB-D\fP] [\fB-F\fP 0|1|2] [\fB-R\fP] [\fB-t\fP \fItableName\fP] [-- \.\.\.]
+.fam T
+.fi
+.SH DESCRIPTION
+\fBpssh2_seq\fP takes an \fIinput\fP sequence (query.fasta) and generates sequence-to-structure
+alignments for this sequence.
+To this end, it starts the two subsequent HHblits runs:
+.IP 1) 4
+build_hhblits_profile: search against uniprot20 database of HMMs and generate a
+HHM output (HMM-profile)
+.IP 2) 4
+scan_structures_hhblits: starting with the HHM output from step 1,
+search against the pdb_full database of HMMs and generate a HHR ouput
+Subsequently, it parses the HHR output from the second run using the
+"parse_hhr_for_pssh2" perl script and generates a .pssh2 file.
+Finally, this outputfile is read into the MySQL database pssh2_local, table pssh2_active,
+using "DB.pssh2_local" to retrieve the access parameters.
+The table pssh2_active_counts keeps track of the generation date of the data, the
+runtime and the number of hits found for the sequence. Negative count number indicate
+error states:
+\fB-1\fP -> build_hhblits_profile, \fB-2\fP -> scan_structures_hhblits, \fB-3\fP -> parse_hhr_for_pssh2,
+\fB-99\fP -> sequence not found
+Any \fIinput\fP not mentioned in options is passed on to 1) and 2).
+The databases to search with hhblits should be available under /var/tmp/rost_db/data/
+unless they are explicitly given in the \fIinput\fP.
+Defaults are configured in /etc/pssh2.conf.
+.SH OPTIONS
+.TP
+.B
+\fB-h\fP
+The option \fB-h\fP displays help and exits.
+.TP
+.B
+\fB-D\fP
+Debug option: do not remove or zip output files
+.TP
+.B
+\fB-F\fP n
+Set force remaking status for making of HMM profile (run build_hhblits_profile):
+.RS
+.TP
+.B
+0
+do not make profile unless none exists
+.TP
+.B
+1
+run only if the profile is older than the last update of uniprot20 (default)
+.TP
+.B
+2
+always run, even if the profile exists
+.RE
+.TP
+.B
+\fB-R\fP
+Retain (DO NOT remake) the HMM profile (same as \fB-F\fP 0)
+.TP
+.B
+\fB-t\fP
+use \fItableName\fP for storing the pssh2 output in the mysql database (default: pssh2_active)
+.TP
+.B
+\fB-s\fP
+Operate silently (passed on to the child scripts.)
+Any other parameters behind "--" are passed on to the child scripts.
+.SH AUTHOR
+Andrea Schafferhans <andrea.schafferhans at rostlab.org>
diff --git a/debian/pssh2.install b/debian/pssh2.install
new file mode 100644
index 0000000..68bf8d1
--- /dev/null
+++ b/debian/pssh2.install
@@ -0,0 +1,15 @@
+build_hhblits_profile usr/bin/
+scan_structures_hhblits usr/bin/
+fasta_to_md5 usr/bin/
+parse_hhr_for_pssh2 usr/bin/
+pssh2_seq usr/bin/
+pp_pssh2 usr/bin/
+pssh2_multi_md5 usr/bin/
+pssh2_aws usr/bin
+get_fasta_for_md5 usr/bin/
+DB.pssh2_local usr/bin/
+DB.aquaria_local usr/bin/
+make_new_pdb_full usr/bin/
+build_hhblits_structure_profile usr/bin/
+find_best_pdb_for_seqres_md5 usr/bin/
+pssh2.conf etc/
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..c30bbdb
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+#
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+#
+# Modified to make a template file for a multi-binary package with separated
+# build-arch and build-indep targets by Bill Allombert 2001
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
+
+%:
+ dh $@
--
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