fragpipe-22.0-0.build.sh

#! /usr/bin/bash

# ------------------------------------------------------------------- Debug

# COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.3; exec bash /dev/shm/runme-$COOKIE.sh
# TESTING=1

# ---------------------------------------------------------------- Preamble

PKG=fragpipe
VERSION=22.0
BUILD=0

# some pipeline parts need python
PYTHONVER=3.11.11

set -e
umask 022

PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/package/bin
PREFIX=/pkg/$PKG-$VERSION-$BUILD
if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi

mkdir -p $PREFIX
cat >$PREFIX/profile <<-EOF
	. /pkg/openjdk-21.0.0.35-0/profile
	PATH=$PREFIX/bin:\$PATH
	# avoid interference with the package/pkg python
	if [ -z "\$PYTHONUSERBASE" ]; then export PYTHONUSERBASE=\$HOME/.local/fragpipe-python ; fi
	if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi
EOF

source $PREFIX/profile

BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.$USER.build.tmp
# keep pip's download cache when testing
test -z "$TESTING" && test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR )
mkdir -p $BUILD_TMPDIR/home
# embedded patches, copy script to an accessible location
cp $0 $BUILD_TMPDIR; ME="$BUILD_TMPDIR/$(basename $0)"
export TMPDIR=$BUILD_TMPDIR
export HOME=$BUILD_TMPDIR/home

NPROC=$(( $(nproc) * 4 / 5 + 1 ))

BUILDDIR=$PREFIX/build

mkdir -p $BUILDDIR
cd $BUILDDIR


# ---------------------------------------------------------------- fragpipe

# the complete installable archive, but permissions are a mess!
# orig: https://github.com/Nesvilab/FragPipe/releases/download/22.0/FragPipe-22.0.zip
BEEHIVE=https://beehive.molgen.mpg.de/e30d93e6c0ef1e2aadd51e732f343451/FragPipe-22.0.zip

test -e FragPipe-$VERSION.zip || wget -nv $BEEHIVE
test -d fragpipe || bsdtar -xf FragPipe-$VERSION.zip

mv fragpipe/bin ..
mv fragpipe/lib ..  # 'libjava' would be smart, but fp uses lib in lookup routines :/
mv fragpipe/tools ..
mv fragpipe/workflows ../workflows_dist

# reset executable attribute in the obvious cases, nerve ...
# some *.py have a shebang, and some ... (you guessed)
# this is safer then accidentally 'defusing' linux binaries within tools
for ext in bat dll exe ico jar obo txt tsv ifl gdb pdb xml json glyc fasta workflow params; do
  find $PREFIX -type f -name "*.$ext" -exec chmod -c 0644 {} \+
done
find $PREFIX -type d -exec chmod -c 0755 {} \+

# set jar mtimes according to content (btw. I didn't know that java was already around in 1980 :)
rm -vf jarredater
sed -ne '/^#Epatch:jarredater/ s/^#Epatch:\S* // p' $ME | patch -p0 --verbose
find $PREFIX -name '*.jar' -exec python jarredater {} \+

(
  # get rid of the way distracting console warning "No interface org.openide.util.spi.SVGLoader instance found"
  cd ../lib
  mkdir -p fixup
  cd fixup
  bsdtar -xf ../org-netbeans-swing-outline-RELEASE200.jar
  rm -v ./org/netbeans/swing/etable/columns.svg # the root cause
  jar -M -c -f org-netbeans-swing-outline-RELEASE200.jar META-INF org
  # alternative ...
  # mv META-INF/MANIFEST.MF .
  # jar -c -f org-netbeans-swing-outline-RELEASE200.jar -m MANIFEST.MF META-INF org
  mv -v org-netbeans-swing-outline-RELEASE200.jar ..
  cd ..
  rm -r fixup
)

# the source archive , some bigger libs missing (diann torch_cpu), permissions here are again messed up
# 'FragPipe-22.0.tar.gz' -> '/src/mariux/md5repo/bfaae508143e0a67b28a6393cbb7b2fb/FragPipe-22.0.tar.gz'
# orig: https://github.com/Nesvilab/FragPipe/archive/refs/tags/22.0.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/bfaae508143e0a67b28a6393cbb7b2fb/FragPipe-22.0.tar.gz

test -e FragPipe-$VERSION.tar.gz || wget -nv $BEEHIVE
test -d FragPipe-$VERSION || tar -xf FragPipe-$VERSION.tar.gz

cd FragPipe-$VERSION

# -------------------------------------------------------------- patch time

# several GUI patches, some are cosmetic, some are related
# to the fact that the installation directory is read only

cd ./MSFragger-GUI

# okay, we have them, so we also like to use them ...
sed -i -e '/^\s\s*public static final int maxProcessors/ s/= 128;/= 256;/' \
       src/com/dmtavt/fragpipe/tabs/TabWorkflow.java

# ... and please do not call home on every start
sed -i \
       -e "/raw.githubusercontent.com/ s|https.*PATH_BUNDLE|file://$PREFIX/etc/Bundle.properties\"|" \
       -e '/^\s\s*+ ".properties"\s*$/ d' \
       src/com/dmtavt/fragpipe/params/ThisAppProps.java

sed -ne '/^#Epatch:FragpipeLocations / s/^#Epatch:\S* // p' $ME | patch -p2 --verbose
sed -ne '/^#Epatch:Fragpipe / s/^#Epatch:\S* // p' $ME | patch -p2 --verbose

# ------------------------------------------------------------- compile now

# a full build, but it will not help with the file attributes, s.a. :/
# result: build/github-release/FragPipe-22.0.zip
#  #> ./gradlew makeReleaseZipNoJre

# debug/devel builds for fragpipe-22.0.jar
#  #> ./gradlew jar --rerun

# only the recompiled gui is needed ...
# result: build/libs/fragpipe-22.0.jar
./gradlew --console plain --max-workers $NPROC jar
mv -v build/libs/fragpipe-22.0.jar $PREFIX/lib

./gradlew --stop # since it is a 'daemon' 

# ---------------------------------------------------------- finish install

cd $PREFIX

mkdir -p etc ltools updates workflows

# the file that is supposed to be downloaded from git-hub
cp -v build/FragPipe-22.0/MSFragger-GUI/src/com/dmtavt/fragpipe/Bundle.properties etc

# this works w/o further installing logging jars:
# JAVA_OPTS=-Dlogback.configurationFile=/package/fragpipe/etc/logback.xml fragpipe
rm -vf etc/logback.xml
sed -ne '/^#Epatch:logback/ s/^#Epatch:\S* // p' $ME | patch -p0 --verbose


# the academic license was acquired by H. Schmidt, some of the tools seem to
# talk with google analytics, just in case you wonder :)
REPO_LICENSED_SOFTWARE=/package/fragpipe/src
cd ltools
cp -p $REPO_LICENSED_SOFTWARE/2024-417_Academic_Research_Use_License_05142024.pdf .
bsdtar -xf $REPO_LICENSED_SOFTWARE/MSFragger-4.1.zip
bsdtar -xf $REPO_LICENSED_SOFTWARE/IonQuant-1.10.27.zip
bsdtar -xf $REPO_LICENSED_SOFTWARE/diaTracer-1.1.5.zip


# create a neater launcher, but also keep the funny one bundled

cat > $PREFIX/bin/mxfragpipe <<- EOF
	#! /usr/bin/bash
	
	set -e
	
	# populate ~/.config/FragPipe/fragpipe/workflows on first start
	
	XDG_CONFIG_HOME="\${XDG_CONFIG_HOME:-\$HOME/.config}"
	export XDG_CONFIG_HOME
	WORKFLOWDIR="\$XDG_CONFIG_HOME/FragPipe/fragpipe/workflows"
	if [ ! -d "\$WORKFLOWDIR" ] ; then # assume first run ...
	  mkdir -vp "\$WORKFLOWDIR"
	  cp --preserve=timestamps /package/fragpipe/workflows.dist/* "\$WORKFLOWDIR"
	  echo 'fragpipe-config.tools-folder=$PREFIX/ltools' >> "\$XDG_CONFIG_HOME/FragPipe/fragpipe/fragpipe-ui.cache"
	fi
	
	
	# avoid stumbling over our filerunner or doublecommander apps
	# grep -l inode/directory /usr/share/applications/*.desktop
	
	if [ ! -e \$XDG_CONFIG_HOME/FragPipe/no_check_filemanager ]; then
	  FILEMANAGER=\$(xdg-mime query default inode/directory)
	  if [[ "\$FILEMANAGER" =~ 'doublecmd' || "\$FILEMANAGER" =~ 'filerunner' ]]; then
	    echo "# ==========================================================================="
	    echo "#"
	    echo "# NOTE: Your default filemanager application is set to \$FILEMANAGER ..."
	    echo "#"
	    echo "#       to fix this issue and switch to thunar, enter:"
	    echo "#       #> xdg-mime default thunar.desktop inode/directory"
	    echo "#"
	    echo "#       to inhibit this message enter:"
	    echo "#       #> touch \$XDG_CONFIG_HOME/FragPipe/no_check_filemanager"
	    echo "#"
	    echo "# ==========================================================================="
	    sleep 5
	    echo "# launching fragpipe now ..."
	    sleep 1
	  fi
	fi
	
	# -classpath '/foobar/lib/*' only adds *.jar files - ohh, what a surprise :)
	exec java \$FRAGPIPE_OPTS \$JAVA_OPTS \\
	          -classpath '$PREFIX/lib/*' \\
	          com.dmtavt.fragpipe.FragPipeMain \\
	          "\${@+\$@}"
EOF

chmod +x $PREFIX/bin/mxfragpipe

echo '# Fragpipe install is done ...'

# ------------------------------------------------------------------ python

cd $BUILDDIR

# -------------------------------------- Use git to track package evolution

test -d .git && rm -rf .git
git init -q; echo -e '[user]\n name = none\n email = of_your_business...' >> .git/config
echo '*' > .gitignore

function piplist() {
  pip list | awk '{ printf("%-36s %s\n", $1,$2) }' | grep -v '\----' > GameOfVersions
}

function track() {
  if [ -d .git ]; then
    if git add -f GameOfVersions; then
      git commit -q -n -m "Package: '$*'" || /bin/true
    fi
  fi
}

function install() {
  echo "# ::INST:: # '${@+$@}'"
  # no-color is nice, but doesn't work when dependencies are installed, so (mis-)use a pipe
  pip install --no-color --compile --cache-dir=$HOME/.cache/pip --prefix=$PREFIX "${@+$@}" | cat
  piplist
  track $*
}


# ---------------------------------------- Build Python & support libraries

(
  # orig: https://www.python.org/ftp/python/3.11.11/Python-3.11.11.tgz
  BEEHIVE=https://beehive.molgen.mpg.de/9a5b43fcc06810b8ae924b0a080e6569/Python-3.11.11.tgz

  test -e Python-$PYTHONVER.tgz || wget -nv $BEEHIVE
  test -d Python-$PYTHONVER || tar -xf Python-$PYTHONVER.tgz
  cd Python-$PYTHONVER

  # BerkeleyDB, the undead ...
  # Newer libgdbm_compat.so versions pull libgdbm.so on their own, our libgdbm_compat.so is older ...
  # So, let setup.py create '-lgdbm -lgdbm_compat' instead of a sole '-lgdbm_compat'
  # verbatim: ndbm_libs = ['gdbm_compat'] => ndbm_libs = ['gdbm','gdbm_compat']
  sed -i -e "/ndbm_libs = / s/_compat'/','gdbm_compat'/" setup.py

  # leave further hints in the log
  sed -i -e  '/db_setup_debug = False/ s/False/True/' \
         -e '/dbm_setup_debug = False/ s/False/True/' setup.py

  # These may come handy if the Python build needs exclusive stuff from $PREFIX
  # INCLUDEDIR=$PREFIX/include \
  # LIBDIR=$PREFIX/lib \
  LDFLAGS="-Wl,-rpath=$PREFIX/lib" \
  ./configure \
          --prefix=$PREFIX \
          --enable-shared

  make -j $NPROC
  make install

  # it might come to happen that something down the line may just call 'python', defuse ...
  test -e $PREFIX/bin/python || ln -s python3 $PREFIX/bin/python

  python -m ensurepip
  pip3 install --prefix=$PREFIX -I pip
  ( # fix 'please update' noise from pip
    cd $PREFIX/lib/python*/site-packages
    sed -ne '/^#Epatch:pip/ s/^#Epatch:\S* // p' $ME | patch -p1 --verbose
  )
  # I hate to do this ...
  ln -s lib $PREFIX/lib64
)
install setuptools
piplist; track START

install Cython
install numpy==1.26.4  # The EasyPQP author nailed numpy to this version (needlessly of course, <2 is the right way ...)
install numba==0.60.0
install wheel

PACKAGES=$(sed -e s/#.*$// <<- __PKGLIST__
	pyopenms==3.2.0
	easypqp==0.1.50
	lxml==5.3.0
	__PKGLIST__
)

for PKG in $PACKAGES; do
  install $PKG
done

# ------------------------------------------------------------ Sanity check

echo "# --------- *** SANITY CHECKS *** ---------"

# I guess it makes sense that files can be read by all users ...
echo "# 1) Check for unreadable files ..."
cd $PREFIX
for D in bin include lib share; do
  find $D \! -perm -004 -exec chmod -c a+r {} +
done

# a cheap one :)
echo "# 2) Running pip check"
pip check

# load all packages, see warnings and spot installation errors
echo "# 3) Module load test."
export NUMEXPR_MAX_THREADS=1
python -c 'help("modules")'
echo "# Note: reached end of load test"

echo "For Deeper checks:"
echo "cd ${BUILDDIR} ;  git log --patch | grep ^[\+\-][^\+\-]"

exit


# -------------------------------------------------------- Included patches

#Epatch:pip # Operation 'Forever young', disable version-check per default.
#Epatch:pip # The option needs to be kept, because some tools make use of
#Epatch:pip # it and would cause pip to fail.
#Epatch:pip --- a/pip/_internal/cli/cmdoptions.py  2022-08-09 17:29:15.853442948 +0200
#Epatch:pip +++ b/pip/_internal/cli/cmdoptions.py  2022-08-10 10:31:35.124945154 +0200
#Epatch:pip @@ -892,7 +892,6 @@
#Epatch:pip      dest="disable_pip_version_check",
#Epatch:pip      action="store_true",
#Epatch:pip -    default=False,
#Epatch:pip -    help="Don't periodically check PyPI to determine whether a new version "
#Epatch:pip -    "of pip is available for download. Implied with --no-index.",
#Epatch:pip +    default=True,
#Epatch:pip +    help="Ignore this option, the version check IS disabled.",
#Epatch:pip  )


#Epatch:jarredater --- jarredater
#Epatch:jarredater +++ jarredater
#Epatch:jarredater @@ -0,0 +1,13 @@
#Epatch:jarredater +import os, sys, time, zipfile
#Epatch:jarredater +
#Epatch:jarredater +dt_list = []
#Epatch:jarredater +if len(sys.argv) > 1:
#Epatch:jarredater +  for f in sys.argv[1:]:
#Epatch:jarredater +    dt_list.clear()
#Epatch:jarredater +    zf = zipfile.ZipFile(f, 'r')
#Epatch:jarredater +    for i in zf.infolist(): dt_list.append(i.date_time)
#Epatch:jarredater +    zf.close()
#Epatch:jarredater +    maxtime = max( dt_list )
#Epatch:jarredater +    print('# touching', f, '->', maxtime)
#Epatch:jarredater +    epo = time.mktime( maxtime + (0,0,0) )
#Epatch:jarredater +    os.utime(f, (epo, epo))


#Epatch:logback --- etc/logback.xml
#Epatch:logback +++ etc/logback.xml
#Epatch:logback @@ -0,0 +1,12 @@
#Epatch:logback +<configuration>
#Epatch:logback +  <!-- enable:  JAVA_OPTS=-Dlogback.configurationFile=/path/to/logback.xml fragpipe -->
#Epatch:logback +  <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
#Epatch:logback +    <encoder>
#Epatch:logback +      <pattern>%d %-5level %-42logger{42} - %msg%n</pattern>
#Epatch:logback +    </encoder>
#Epatch:logback +  </appender>
#Epatch:logback +  <logger name="com.dmtavt.fragpipe.api.FragpipeCacheUtils" level="error" />
#Epatch:logback +  <root level="debug">
#Epatch:logback +    <appender-ref ref="STDOUT" />
#Epatch:logback +  </root>
#Epatch:logback +</configuration>


### =========================================================================================
### VERY CAREFUL NOW, we are patchin WinDos files, lookout for '<cr>' / '^M' in your editor !
### =========================================================================================

#Epatch:FragpipeLocations diff --git a/MSFragger-GUI/src/com/dmtavt/fragpipe/FragpipeLocations.java b/MSFragger-GUI/src/com/dmtavt/fragpipe/FragpipeLocations.java
#Epatch:FragpipeLocations index 6f14590e..58f56d5f 100644
#Epatch:FragpipeLocations --- a/MSFragger-GUI/src/com/dmtavt/fragpipe/FragpipeLocations.java
#Epatch:FragpipeLocations +++ b/MSFragger-GUI/src/com/dmtavt/fragpipe/FragpipeLocations.java
#Epatch:FragpipeLocations @@ -106,8 +106,9 @@ public class FragpipeLocations {
#Epatch:FragpipeLocations          tools = dir.resolve(Paths.get("../tools"));
#Epatch:FragpipeLocations        }
#Epatch:FragpipeLocations  
#Epatch:FragpipeLocations -      Path workflows = dir.resolve("../workflows");
#Epatch:FragpipeLocations -      Path longTermStorage = CacheUtils.getTempDir();
#Epatch:FragpipeLocations +      // Path workflows = dir.resolve("../workflows");
#Epatch:FragpipeLocations +      Path workflows = dir.resolve( CacheUtils.getTempDir().toString() + "/workflows" );
#Epatch:FragpipeLocations +      Path longTermStorage = CacheUtils.getTempDir(); // well this yields to > XDG_CONFIG_HOME + "/FragPipe" <
#Epatch:FragpipeLocations  
#Epatch:FragpipeLocations        // create locations if they don't yet exist
#Epatch:FragpipeLocations        List<Path> paths = Arrays.asList(dir, cache, tools, workflows, longTermStorage);


#Epatch:Fragpipe diff --git a/MSFragger-GUI/src/com/dmtavt/fragpipe/Fragpipe.java b/MSFragger-GUI/src/com/dmtavt/fragpipe/Fragpipe.java
#Epatch:Fragpipe index 16fd82ec..64696321 100644
#Epatch:Fragpipe --- a/MSFragger-GUI/src/com/dmtavt/fragpipe/Fragpipe.java
#Epatch:Fragpipe +++ b/MSFragger-GUI/src/com/dmtavt/fragpipe/Fragpipe.java
#Epatch:Fragpipe @@ -289,22 +289,36 @@ public class Fragpipe extends JFrameHeadless {
#Epatch:Fragpipe      log.debug("Saving ui cache: collected {} properties from UI. Size after merging with cached object: {}.",
#Epatch:Fragpipe          tabsAsProps.size(), cache.propsUiState.size());
#Epatch:Fragpipe      try {
#Epatch:Fragpipe -      cache.propsUiState.setPath(FragpipeLocations.get().getPathUiCache(false));
#Epatch:Fragpipe -      cache.propsUiState.save();
#Epatch:Fragpipe +      // when we fail here (lib/../cache), the other one will not be written out :/
#Epatch:Fragpipe +      //cache.propsUiState.setPath(FragpipeLocations.get().getPathUiCache(false));
#Epatch:Fragpipe +      //cache.propsUiState.save();
#Epatch:Fragpipe        cache.propsUiState.setPath(FragpipeLocations.get().getPathUiCache(true));
#Epatch:Fragpipe        cache.propsUiState.save();
#Epatch:Fragpipe      } catch (IOException ex) {
#Epatch:Fragpipe -      log.error("Error saving ui cache. It won't affect the results.");
#Epatch:Fragpipe +      log.error("Error saving ui cache. It won't affect the results." + " (" +
#Epatch:Fragpipe +                 FragpipeLocations.get().getPathUiCache(true) + ")"
#Epatch:Fragpipe +      );
#Epatch:Fragpipe      }
#Epatch:Fragpipe      try {
#Epatch:Fragpipe -      cache.propsRuntime.setPath(FragpipeLocations.get().getPathRuntimeCache(false));
#Epatch:Fragpipe -      cache.propsRuntime.save();
#Epatch:Fragpipe +      // when we fail here (lib/../cache), the other one will not be written out :/
#Epatch:Fragpipe +      //cache.propsRuntime.setPath(FragpipeLocations.get().getPathRuntimeCache(false));
#Epatch:Fragpipe +      //cache.propsRuntime.save();
#Epatch:Fragpipe        cache.propsRuntime.setPath(FragpipeLocations.get().getPathRuntimeCache(true));
#Epatch:Fragpipe        cache.propsRuntime.save();
#Epatch:Fragpipe      } catch (IOException ex) {
#Epatch:Fragpipe -      log.error("Error saving runtime cache. It won't affect the results.");
#Epatch:Fragpipe +      log.error("Error saving runtime cache. It won't affect the results." + " (" +
#Epatch:Fragpipe +                 FragpipeLocations.get().getPathRuntimeCache(true) + ")"
#Epatch:Fragpipe +      );
#Epatch:Fragpipe      }
#Epatch:Fragpipe  
#Epatch:Fragpipe +  /*
#Epatch:Fragpipe +
#Epatch:Fragpipe +    -- skipping this for the moment --
#Epatch:Fragpipe +
#Epatch:Fragpipe +     - copy the existing workflows on first start (done by the starter script)
#Epatch:Fragpipe +     - then use the users XDG_CONFIG_HOME/FragPipe/fragpipe/workflows directory
#Epatch:Fragpipe +       as the sole source for workflows
#Epatch:Fragpipe +
#Epatch:Fragpipe      // saving workflows
#Epatch:Fragpipe      Path dirWorkflows = FragpipeLocations.get().getDirWorkflows();
#Epatch:Fragpipe      Path lts = FragpipeLocations.get().getPathLongTermStorage().resolve(dirWorkflows.getFileName());
#Epatch:Fragpipe @@ -315,6 +329,8 @@ public class Fragpipe extends JFrameHeadless {
#Epatch:Fragpipe        log.error("Error saving workflows between sessions.");
#Epatch:Fragpipe        throw new IllegalStateException(e);
#Epatch:Fragpipe      }
#Epatch:Fragpipe +  */
#Epatch:Fragpipe +
#Epatch:Fragpipe    }
#Epatch:Fragpipe  
#Epatch:Fragpipe    public static FormEntry.Builder fe(JComponent comp, String compName) {
#Epatch:Fragpipe @@ -385,9 +401,11 @@ public class Fragpipe extends JFrameHeadless {
#Epatch:Fragpipe        System.exit(1);
#Epatch:Fragpipe      }
#Epatch:Fragpipe  
#Epatch:Fragpipe +    /* why are linux users forced to use 'Nimbus' ?
#Epatch:Fragpipe      if (!headless) {
#Epatch:Fragpipe        SwingUtils.setLaf();
#Epatch:Fragpipe      }
#Epatch:Fragpipe +    */
#Epatch:Fragpipe  
#Epatch:Fragpipe      FragpipeLoader fragpipeLoader = new FragpipeLoader();
#Epatch:Fragpipe      Bus.register(fragpipeLoader);