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[{dirs}} in lib/syscfg.d/ contains invocations commands for third-party executables EPrints might need to use. In particular the following invocations:

my %invocations = (
  'convert_crop_white' => '$(convert) -crop 0x0 -bordercolor white -border 4x4 $(SOURCE) $(TARGET)',
  'dvips' => '$(dvips) $(SOURCE) -o $(TARGET)',
  'sendmail' => '$(sendmail) -oi -t -odb --',
  'elinks' => '$(elinks) -dump 1 -dump-charset UTF-8 $(SOURCE) > $(TARGET)',
  'latex' => '$(latex) -no-shell-escape -output-directory=$(TARGET) $(SOURCE)',
  'targz' => '$(gunzip) -c < $(ARC) 2>/dev/null | $(tar) xf - -C $(DIR) >/dev/null 2>&1',
  'antiwordpdf' => '$(antiword) -a a4 -m 8859-1 $(SOURCE) > $(TARGET)',
  'pdftotext' => '$(pdftotext) -enc UTF-8 -layout $(SOURCE) $(TARGET)',
  'zip' => '$(unzip) 1>/dev/null 2>&1 -qq -o -d $(DIR) $(ARC)',
  'unzip' => '$(unzip) 1>/dev/null 2>&1 -qq -o -j -d $(DIRECTORY) $(SOURCE)',
  'cpall' => '$(cp) -pR $(SOURCE)/* $(TARGET)',
  'wget' => '$(wget) -U "Mozilla/5.0" -r -L -q -m -nH -np --execute="robots=off" --cut-dirs=$(CUTDIRS) --content-disposition $(URL)',
  'antiword' => '$(antiword) -t -f -m UTF-8 $(SOURCE) > $(TARGET)',
  'doc2txt' => '$(perl) $(doc2txt) $(SOURCE) $(TARGET)',
  'rmall' => '$(rm) -rf $(TARGET)/*',
  'ffmpeg_i' => '$(ffmpeg) -i $(SOURCE)',
  'ffmpeg_video_mp4' => '$(ffmpeg) -y -i $(SOURCE) -acodec $(audio_codec) -strict -2 -ac 2 -ar $(audio_sampling) -ab $(audio_bitrate) -f $(container) -vcodec $(video_codec) -r $(video_frame_rate) -b:v $(video_bitrate) -s $(width)x$(height) $(TARGET)',
  'ffmpeg_video_ogg' => '$(ffmpeg) -y -i $(SOURCE) -acodec $(audio_codec) -ac 2 -ar $(audio_sampling) -ab $(audio_bitrate) -f $(container) -vcodec $(video_codec) -r $(video_frame_rate) -b:v $(video_bitrate) -s $(width)x$(height) $(TARGET)',
  'ffmpeg_video_webm'=> '$(ffmpeg) -y -i $(SOURCE) -acodec $(audio_codec) -ac 2 -ar $(audio_sampling) -ab $(audio_bitrate) -f $(container) -vcodec $(video_codec) -r $(video_frame_rate) -b:v $(video_bitrate) -s $(width)x$(height) $(TARGET)',
  'ffmpeg_audio_mp4' => '$(ffmpeg) -y -i $(SOURCE) -acodec $(audio_codec) -strict -2 -ac 2 -ar $(audio_sampling) -ab $(audio_bitrate) -f $(container) $(TARGET)',
  'ffmpeg_audio_ogg' => '$(ffmpeg) -y -i $(SOURCE) -acodec $(audio_codec) -ac 2 -ar $(audio_sampling) -ab $(audio_bitrate) -f $(container) $(TARGET)',
  'ffmpeg_cell' => '$(ffmpeg) -y -i $(SOURCE) -an -f mjpeg -ss $(offset) -t 00:00:01 -r 1 -s $(width)x$(height) $(TARGET)',
  'unoconv' => '$(unoconv) -f $(FORMAT) $(SOURCE)',
  'txt2refs' => '$(perl) $(txt2refs) $(SOURCE) $(TARGET)',
  'ffprobe' => '$(ffprobe) -show_streams $(SOURCE)',

It may be necessary to modify some of these if you have special requirements. Typically, FFMPEG invocations need to be changed from time to time.