actually add Flye binaries for real -_-'

bin/Flye-2.9/lib/samtools-1.9/config.h

@@ -0,0 +1,72 @@
+/* config.h.  Generated from config.h.in by configure.  */
+/* config.h.in.  Generated from configure.ac by autoheader.  */
+
+/* If you use configure, this file provides #defines reflecting your
+   configuration choices.  If you have not run configure, suitable
+   conservative defaults will be used.
+
+   Autoheader adds a number of items to this template file that are not
+   used by samtools: STDC_HEADERS and most HAVE_*_H header file defines
+   are immaterial, as we assume standard ISO C headers and facilities;
+   the PACKAGE_* defines are unused and are overridden by the more
+   accurate PACKAGE_VERSION as computed by the Makefile.  */
+
+/* Define to 1 if a SysV or X/Open compatible Curses library is present */
+/* #undef HAVE_CURSES */
+
+/* Define to 1 if library supports color (enhanced functions) */
+/* #undef HAVE_CURSES_COLOR */
+
+/* Define to 1 if library supports X/Open Enhanced functions */
+/* #undef HAVE_CURSES_ENHANCED */
+
+/* Define to 1 if <curses.h> is present */
+/* #undef HAVE_CURSES_H */
+
+/* Define to 1 if library supports certain obsolete features */
+/* #undef HAVE_CURSES_OBSOLETE */
+
+/* Define to 1 if you have the `z' library (-lz). */
+#define HAVE_LIBZ 1
+
+/* Define to 1 if the Ncurses library is present */
+/* #undef HAVE_NCURSES */
+
+/* Define to 1 if the NcursesW library is present */
+/* #undef HAVE_NCURSESW */
+
+/* Define to 1 if <ncursesw/curses.h> is present */
+/* #undef HAVE_NCURSESW_CURSES_H */
+
+/* Define to 1 if <ncursesw.h> is present */
+/* #undef HAVE_NCURSESW_H */
+
+/* Define to 1 if <ncurses/curses.h> is present */
+/* #undef HAVE_NCURSES_CURSES_H */
+
+/* Define to 1 if <ncurses.h> is present */
+/* #undef HAVE_NCURSES_H */
+
+/* Define to the address where bug reports for this package should be sent. */
+#define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net"
+
+/* Define to the full name of this package. */
+#define PACKAGE_NAME "Samtools"
+
+/* Define to the full name and version of this package. */
+#define PACKAGE_STRING "Samtools 1.9"
+
+/* Define to the one symbol short name of this package. */
+#define PACKAGE_TARNAME "samtools"
+
+/* Define to the home page for this package. */
+#define PACKAGE_URL "http://www.htslib.org/"
+
+/* Define to the version of this package. */
+#define PACKAGE_VERSION "1.9"
+
+/* Number of bits in a file offset, on hosts where this is settable. */
+/* #undef _FILE_OFFSET_BITS */
+
+/* Define for large files, on AIX-style hosts. */
+/* #undef _LARGE_FILES */

bin/Flye-2.9/lib/samtools-1.9/config.log

@@ -0,0 +1,255 @@
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by Samtools configure 1.9, which was
+generated by GNU Autoconf 2.68.  Invocation command line was
+
+  $ ./configure --without-curses --disable-bz2 --disable-lzma --enable-plugins
+
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = localhost.localdomain
+uname -m = x86_64
+uname -r = 3.10.0-1160.45.1.el7.x86_64
+uname -s = Linux
+uname -v = #1 SMP Wed Oct 13 17:20:51 UTC 2021
+
+/usr/bin/uname -p = x86_64
+/bin/uname -X     = unknown
+
+/bin/arch              = x86_64
+/usr/bin/arch -k       = unknown
+/usr/convex/getsysinfo = unknown
+/usr/bin/hostinfo      = unknown
+/bin/machine           = unknown
+/usr/bin/oslevel       = unknown
+/bin/universe          = unknown
+
+PATH: /usr/local/bin
+PATH: /usr/local/sbin
+PATH: /usr/bin
+PATH: /usr/sbin
+PATH: /bin
+PATH: /sbin
+PATH: /home/fer/.local/bin
+PATH: /home/fer/bin
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+configure:2153: checking for gcc
+configure:2169: found /usr/bin/gcc
+configure:2180: result: gcc
+configure:2409: checking for C compiler version
+configure:2418: gcc --version >&5
+gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
+Copyright (C) 2015 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+configure:2429: $? = 0
+configure:2418: gcc -v >&5
+Using built-in specs.
+COLLECT_GCC=gcc
+COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
+Thread model: posix
+gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) 
+configure:2429: $? = 0
+configure:2418: gcc -V >&5
+gcc: error: unrecognized command line option '-V'
+gcc: fatal error: no input files
+compilation terminated.
+configure:2429: $? = 4
+configure:2418: gcc -qversion >&5
+gcc: error: unrecognized command line option '-qversion'
+gcc: fatal error: no input files
+compilation terminated.
+configure:2429: $? = 4
+configure:2449: checking whether the C compiler works
+configure:2471: gcc   -lz -L/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/minimap2 -lminimap2 conftest.c  >&5
+configure:2475: $? = 0
+configure:2523: result: yes
+configure:2526: checking for C compiler default output file name
+configure:2528: result: a.out
+configure:2534: checking for suffix of executables
+configure:2541: gcc -o conftest   -lz -L/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/minimap2 -lminimap2 conftest.c  >&5
+configure:2545: $? = 0
+configure:2567: result: 
+configure:2589: checking whether we are cross compiling
+configure:2597: gcc -o conftest   -lz -L/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/minimap2 -lminimap2 conftest.c  >&5
+configure:2601: $? = 0
+configure:2608: ./conftest
+configure:2612: $? = 0
+configure:2627: result: no
+configure:2632: checking for suffix of object files
+configure:2654: gcc -c   conftest.c >&5
+configure:2658: $? = 0
+configure:2679: result: o
+configure:2683: checking whether we are using the GNU C compiler
+configure:2702: gcc -c   conftest.c >&5
+configure:2702: $? = 0
+configure:2711: result: yes
+configure:2720: checking whether gcc accepts -g
+configure:2740: gcc -c -g  conftest.c >&5
+configure:2740: $? = 0
+configure:2781: result: yes
+configure:2798: checking for gcc option to accept ISO C89
+configure:2862: gcc  -c -g -O2  conftest.c >&5
+configure:2862: $? = 0
+configure:2875: result: none needed
+configure:2904: checking for special C compiler options needed for large files
+configure:2949: result: no
+configure:2955: checking for _FILE_OFFSET_BITS value needed for large files
+configure:2980: gcc -c -g -O2  conftest.c >&5
+configure:2980: $? = 0
+configure:3012: result: no
+configure:3145: checking location of HTSlib source tree
+configure:3166: result: htslib-1.9
+configure:4134: checking for zlib.h
+configure:4134: gcc -c -g -O2  conftest.c >&5
+configure:4134: $? = 0
+configure:4134: result: yes
+configure:4143: checking for inflate in -lz
+configure:4168: gcc -o conftest -g -O2  -lz -L/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/minimap2 -lminimap2 conftest.c -lz   >&5
+configure:4168: $? = 0
+configure:4177: result: yes
+configure:4203: checking for library containing regcomp
+configure:4234: gcc -o conftest -g -O2  -lz -L/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/minimap2 -lminimap2 conftest.c  >&5
+configure:4234: $? = 0
+configure:4251: result: none required
+configure:4389: creating ./config.status
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by Samtools config.status 1.9, which was
+generated by GNU Autoconf 2.68.  Invocation command line was
+
+  CONFIG_FILES    = 
+  CONFIG_HEADERS  = 
+  CONFIG_LINKS    = 
+  CONFIG_COMMANDS = 
+  $ ./config.status 
+
+on localhost.localdomain
+
+config.status:805: creating config.mk
+config.status:805: creating config.h
+configure:5626: === configuring in htslib-1.9 (/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/samtools-1.9/htslib-1.9)
+configure:5689: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  '--without-curses' '--disable-bz2' '--disable-lzma' '--enable-plugins' 'LDFLAGS=-lz -L/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/minimap2 -lminimap2' --cache-file=/dev/null --srcdir=.
+
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+
+ac_cv_c_compiler_gnu=yes
+ac_cv_env_CC_set=
+ac_cv_env_CC_value=
+ac_cv_env_CFLAGS_set=
+ac_cv_env_CFLAGS_value=
+ac_cv_env_CPPFLAGS_set=
+ac_cv_env_CPPFLAGS_value=
+ac_cv_env_CURSES_LIB_set=
+ac_cv_env_CURSES_LIB_value=
+ac_cv_env_LDFLAGS_set=set
+ac_cv_env_LDFLAGS_value='-lz -L/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/minimap2 -lminimap2'
+ac_cv_env_LIBS_set=
+ac_cv_env_LIBS_value=
+ac_cv_env_build_alias_set=
+ac_cv_env_build_alias_value=
+ac_cv_env_host_alias_set=
+ac_cv_env_host_alias_value=
+ac_cv_env_target_alias_set=
+ac_cv_env_target_alias_value=
+ac_cv_header_zlib_h=yes
+ac_cv_lib_z_inflate=yes
+ac_cv_objext=o
+ac_cv_prog_ac_ct_CC=gcc
+ac_cv_prog_cc_c89=
+ac_cv_prog_cc_g=yes
+ac_cv_search_regcomp='none required'
+ac_cv_sys_file_offset_bits=no
+ac_cv_sys_largefile_CC=no
+ax_cv_htslib=yes
+ax_cv_htslib_which=source
+
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+
+CC='gcc'
+CFLAGS='-g -O2'
+CPPFLAGS=''
+CURSES_LIB=''
+DEFS='-DHAVE_CONFIG_H'
+ECHO_C=''
+ECHO_N='-n'
+ECHO_T=''
+EXEEXT=''
+HTSDIR='htslib-1.9'
+HTSLIB_CPPFLAGS='-Ihtslib-1.9'
+HTSLIB_LDFLAGS='-Lhtslib-1.9'
+Hinstall='#'
+Hsource=''
+LDFLAGS='-lz -L/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/minimap2 -lminimap2'
+LIBOBJS=''
+LIBS=''
+LTLIBOBJS=''
+OBJEXT='o'
+PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net'
+PACKAGE_NAME='Samtools'
+PACKAGE_STRING='Samtools 1.9'
+PACKAGE_TARNAME='samtools'
+PACKAGE_URL='http://www.htslib.org/'
+PACKAGE_VERSION='1.9'
+PATH_SEPARATOR=':'
+SHELL='/bin/sh'
+ac_ct_CC='gcc'
+bindir='${exec_prefix}/bin'
+build_alias=''
+datadir='${datarootdir}'
+datarootdir='${prefix}/share'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+dvidir='${docdir}'
+exec_prefix='${prefix}'
+host_alias='unknown-Linux'
+htmldir='${docdir}'
+includedir='${prefix}/include'
+infodir='${datarootdir}/info'
+libdir='${exec_prefix}/lib'
+libexecdir='${exec_prefix}/libexec'
+localedir='${datarootdir}/locale'
+localstatedir='${prefix}/var'
+mandir='${datarootdir}/man'
+oldincludedir='/usr/include'
+pdfdir='${docdir}'
+prefix='/usr/local'
+program_transform_name='s,x,x,'
+psdir='${docdir}'
+sbindir='${exec_prefix}/sbin'
+sharedstatedir='${prefix}/com'
+subdirs=' htslib-1.9'
+sysconfdir='${prefix}/etc'
+target_alias=''
+
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+
+/* confdefs.h */
+#define PACKAGE_NAME "Samtools"
+#define PACKAGE_TARNAME "samtools"
+#define PACKAGE_VERSION "1.9"
+#define PACKAGE_STRING "Samtools 1.9"
+#define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net"
+#define PACKAGE_URL "http://www.htslib.org/"
+#define HAVE_LIBZ 1
+
+configure: exit 0

bin/Flye-2.9/lib/samtools-1.9/config.mk

@@ -0,0 +1,54 @@
+#  Optional configure Makefile overrides for samtools.
+#
+#    Copyright (C) 2015,2017 Genome Research Ltd.
+#
+#    Author: John Marshall <jm18@sanger.ac.uk>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+# This is config.mk.  Generated from config.mk.in by configure.
+#
+# If you use configure, this file overrides variables and augments rules
+# in the Makefile to reflect your configuration choices.  If you don't run
+# configure, the main Makefile contains suitable conservative defaults.
+
+prefix       = /usr/local
+exec_prefix  = ${prefix}
+bindir       = ${exec_prefix}/bin
+datarootdir  = ${prefix}/share
+mandir       = ${datarootdir}/man
+
+CC       = gcc
+CPPFLAGS = 
+CFLAGS   = -g -O2
+LDFLAGS  = -lz -L/home/fer/opt/SqueezeMeta/bin/Flye-2.9/lib/minimap2 -lminimap2
+LIBS     = 
+
+HTSDIR = htslib-1.9
+include $(HTSDIR)/htslib.mk
+include $(HTSDIR)/htslib_static.mk
+HTSLIB = $(HTSDIR)/libhts.a
+HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
+HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
+BGZIP = $(HTSDIR)/bgzip
+HTSLIB_CPPFLAGS = -Ihtslib-1.9
+#HTSLIB_LDFLAGS = -Lhtslib-1.9
+#HTSLIB_LIB = -lhts
+
+CURSES_LIB =