1  ls
    2  ls ..
    3  pwd
    4  ls
    5  cd ..
    6  ls
    7  cd ..
    8  ls
    9  ls tmp/
   10  ls etc/
   11  ls
   12  ls 
   13  ls irene-enhancers/
   14  ls irene-enhancers/irene
   15  cd irene-enhancers/irene-enhancers/
   16  ls
   17  ls asmMappings/
   18  ls
   19  ls ireneIdsKeys/
   20  ls
   21  pwd
   22  ls
   23  ls asmMappings/
   24  pwd
   25  scp -r asmMappings $hgwdev:/cluster/home/markd/compbio/compartiveGenomics/projs/zoonomia-irene/
   26  pwd
   27  ls
   28  pwd
   29  cd ll
   30  ls
   31  cd ..
   32  ls
   33  cd ..
   34  ls
   35  pwd
   36  ls
   37  ls etc/
   38  ls irene-enhancers/
   39  ls irene-enhancers/irene
   40  ls irene-enhancers/irene-enhancers/
   41  pwd
   42  cd ..
   43  ls
   44  pwd
   45  ls
   46  cd ..
   47  ls
   48  cd cactus/241-mammalian-2020v2-hub/
   49  ls
   50  pwd
   51  pwd -P
   52  pwd
   53  pushd ..
   54  ls
   55  pwd
   56  dirs
   57  ls
   58  popd
   59  ls
   60  pwd
   61  pwd -P
   62  ls
   63  pwd
   64  pushd
   65  ls
   66  find . -name '*.chromAlias*'
   67  gps tar
   68  pwd
   69  pushd
   70  popd
   71  pushd ~/cgl-data/cactus/
   72  ls
   73  cd 241-mammalian-2020v2-hub/
   74  git pull
   75  git pullushd
   76  pushd
   77  git pull
   78  pushd
   79  ls
   80  pwd
   81  git pull
   82  get push
   83  pushd
   84  git pull
   85  pwd
   86  cd ~/compbio/
   87  ls
   88  df
   89  cd /nanopore/cgl/
   90  ls
   91  df -l
   92  df -hx tmps
   93  df -hx tmfs
   94  df -h -x tmfs
   95  df -h -x tmpfs
   96  cd /data/
   97  cd /nanopore/
   98  cd cgl/
   99  ls -ld.
  100  ls -ld .
  101  pwd
  102  l
  103  ls data/
  104  f prajna
  105  id prajna
  106  id pnhebbar
  107  pwd
  108  mkdir users
  109  ls -ld users/
  110  chmod a+w users/
  111  cd users/
  112  pwd
  113  ls /data/
  114  ls /nanopore/dan/
  115  ls /nanopore/cgl/
  116  ls /nanopore/cgl/data/
  117  ls /nanopore/cgl/data/cactus/
  118  ls /nanopore/cgl/data/cactus/ *.hal
  119  l /nanopore/cgl/data/cactus/ *.hal
  120  l /nanopore/cgl/data/cactus/*.hal
  121  l /nanopore/cgl/data/cactus/241-mammalian-2020v2.1.hal
  122  l -hd /nanopore/cgl/data/cactus/241-mammalian-2020v2.1.hal
  123  pwd
  124  ls ~/opt/current/x86_64/bin/python3
  125  pushd ~/tmp/
  126  ls
  127  mv * old/
  128  wget -nv https://www.python.org/ftp/python/3.11.0/Python-3.11.0.tar.xz
  129  tar -xf Python-3.11.0.tar.xz 
  130       (  CXXFLAGS='-D_GLIBCXX_USE_CXX11_ABI=1'; LDFLAGS="-L${MED_OPT}/lib -Wl,-rpath -Wl,${MED_OPT}/lib"  CPPFLAGS=-I${MED_OPT}/include PKG_CONFIG_PATH="${MED_OPT}/lib/pkgconfig:${MED_OPT}/share/pkgconfig:/usr/share/pkgconfig:/usr/lib/pkgconfig" ./configure --enable-cxx --prefix=${MED_OPT} && nice make V=1 -j 20  && make V=1 install)>&build.out &
  131  pwd
  132  cd Python-3.11.0/
  133       (  CXXFLAGS='-D_GLIBCXX_USE_CXX11_ABI=1'; LDFLAGS="-L${MED_OPT}/lib -Wl,-rpath -Wl,${MED_OPT}/lib"  CPPFLAGS=-I${MED_OPT}/include PKG_CONFIG_PATH="${MED_OPT}/lib/pkgconfig:${MED_OPT}/share/pkgconfig:/usr/share/pkgconfig:/usr/lib/pkgconfig" ./configure --enable-cxx --prefix=${MED_OPT} && nice make V=1 -j 20  && make V=1 install)>&build.out &
  134  jobs
  135  pushd ~/compbio/code/pycbio/
  136  ls
  137  git pull
  138  pwd
  139  ls
  140  jobs
  141  ls
  142  pushd /nanopore/
  143  ls
  144  ls -ld .
  145  f ann
  146  id anmmccar
  147  l
  148  ls HL/
  149  pwd
  150  id anmmccar
  151  pwd
  152  popd
  153  ls
  154  rehash
  155  python --version
  156  python3 --version
  157  python3 -m pip install virtualenv
  158  pushd
  159  python3
  160  pwd
  161  ls
  162  ssl
  163  openssl
  164  openssl --version
  165  openssl -v
  166  openssl version
  167  ~markd/opt/current/x86_64/bin/python3.9 -m virtualenv
  168  ~markd/opt/current/x86_64/bin/python3.9 -m pip install virtualenv
  169  ~markd/opt/current/x86_64/bin/python3.9 -m pip install --upgrade pip
  170  pwd
  171  make distclean
  172       (  CXXFLAGS='-D_GLIBCXX_USE_CXX11_ABI=1'; LDFLAGS="-L${MED_OPT}/lib -Wl,-rpath -Wl,${MED_OPT}/lib"  CPPFLAGS=-I${MED_OPT}/include PKG_CONFIG_PATH="${MED_OPT}/lib/pkgconfig:${MED_OPT}/share/pkgconfig:/usr/share/pkgconfig:/usr/lib/pkgconfig" ./configure --enable-cxx --prefix=${MED_OPT} && nice make V=1 -j 30  && make V=1 install)>&build.out &
  173  psi
  174  cat l
  175  pwd
  176  ls
  177  pushd ~/compbio/
  178  ls
  179  cd browser/
  180  ls
  181  cd /public/groups/
  182  ls
  183  cd cgl/
  184  ls
  185  cd local/
  186  ls
  187  ls bin/
  188  pwd
  189  cd build/
  190  wget https://downloads.globus.org/globus-connect-personal/linux/stable/globusconnectpersonal-latest.tgz
  191  ls
  192  tar -tf globusconnectpersonal-latest.tgz 
  193  which globusconnect
  194  l /public/home/markd/opt/centos7.0/x86_64/bin/globusconnect 
  195  pwd
  196  ls
  197  tar -xf globusconnectpersonal-latest.tgz &
  198  ls ..
  199  ls
  200  pwd
  201  mkdir ../libexec
  202  mv globusconnectpersonal-3.2.0 ../libexec/
  203  cd ../bin/
  204  ls ../libexec/globusconnectpersonal-3.2.0/
  205  l ../libexec/globusconnectpersonal-3.2.0/globusconnect
  206  ln -s ../libexec/globusconnectpersonal-3.2.0/globusconnect .
  207  ./globusconnect 
  208  pwd
  209  cd ~/.config/
  210  ls
  211  cd ..
  212  ls
  213  pwd
  214  ls .globus.cfg 
  215  pwd
  216  pushd ~/tmp/Python-3.11.0/
  217  python3 --version
  218  python3 -m ssl
  219  pwd
  220  ls
  221  make distclean
  222  (LDFLAGS="-L${MED_OPT}/lib -Wl,-rpath -Wl,${MED_OPT}/lib"  CPPFLAGS=-I${MED_OPT}/include PKG_CONFIG_PATH="${MED_OPT}/lib/pkgconfig:${MED_OPT}/share/pkgconfig:/usr/share/pkgconfig:/usr/lib/pkgconfig" ./configure --prefix=${MED_OPT} && nice mmake  && mmake install)>&build.out & 
  223  psi
  224  ls
  225  openssl version
  226  rehash
  227  which openssl
  228  openssl version
  229  openssl11 
  230  openssl11 verison
  231  openssl11 
  232  ls /otpwd
  233  ls
  234  mmake distclean
  235  ./configure --help
  236  pwd
  237  pls
  238  (LDFLAGS="-L${MED_OPT}/lib -Wl,-rpath -Wl,${MED_OPT}/lib"  CPPFLAGS=-I${MED_OPT}/include PKG_CONFIG_PATH="${MED_OPT}/lib/pkgconfig:${MED_OPT}/share/pkgconfig:/usr/share/pkgconfig:/usr/lib/pkgconfig" ./configure --prefix=${MED_OPT}   --with-openssl=/usr/include/openssl11/ )>&conf.out
  239  pwd
  240  popd
  241  cd ~/tmp/
  242  ls
  243  mv * old/
  244  rm -rf old/&
  245  pwd
  246  popd
  247  pushd
  248  pod
  249  popd
  250  ls
  251  command dirs
  252  pwd
  253  git status
  254  got commit -am 'link in primate phast cons'
  255  git commit -am 'link in primate phast cons'
  256  git push
  257  pwd
  258  cd ..
  259  ls
  260  cd ..
  261  ls
  262  ./makeBackup >&log
  263  bg
  264  l /nanopore/cgl/data/cactus/
  265  pwd
  266  l /public/home/markd/cgl-data/cactus/447-mammalian-2022v1*
  267  a
  268  pwd
  269  ls
  270  pwd
  271  pushd
  272  pushd cactus/
  273  ls
  274  cd work/
  275  ls
  276  cd test-hubs/
  277  ls
  278  cd 241-mammalian-2020v2-test-hub/
  279  ls
  280  git pull
  281  egrep '^group' */*track.Db.txt
  282  egrep '^group' */*trackDb.txt
  283  egrep '^group' */*trackDb.txt >~/tmp/grps
  284  pwd
  285  egrep 'group ' */*trackDb.txt >~/tmp/grps
  286  pwd
  287  popd
  288  cd cactus/241-mammalian-2020v2-hub/
  289  git modified
  290  git commit -am 'moved tracks from other to zoonomia group'
  291  git push
  292  pwd
  293  ls
  294  pwd
  295  cd ..
  296  ls
  297  cd ..
  298  ls
  299  cd cactus/
  300  cd ..
  301  pwd
  302  ls
  303  ./makeBackup 
  304  5888955
  305  ./makeBackup 
  306  pwd
  307  ls
  308  cd cactus/
  309  ls
  310  l
  311  ls
  312  halStats -genomes
  313  halStats -genomes 447-mammalian-2022v1.hal
  314  halStats --genomes 447-mammalian-2022v1.hal
  315  halStats --genomes 447-mammalian-2022v1.hal | sort > ~/tmp/new.lst
  316  sort 241-mammalian-2020v2.genomes >~/tmp/old.lst
  317  pushd ~/tmp/
  318  diff old.lst new.lst >pri.lst
  319  mv new.lst up.lst
  320  sort -u up.lst >x
  321  mv x up.lst 
  322  diff old.lst new.lst >pri.lst
  323  diff old.lst up.lst >pri.lst
  324  pwd
  325  popd
  326  ls
  327  find . -name '*.mod'
  328  pwd
  329  ls
  330  find . -name '*.nh'
  331  pwd
  332  mv ~/tmp/241-mammals-human-phylop-models .
  333  l 241-mammals-human-phylop-models/
  334  l -d 241-mammals-human-phylop-models/
  335  pwd
  336  rm -rf 241-mammals-human-phylop-models/
  337  pwd
  338  mv ~/tmp/241-mammals-human-phylop-models/ .
  339  pwd
  340  ls 241-mammals-human-phylop-models/
  341  ls
  342  ls /nanopore/cgl/glenn-scratch/split
  343  pwd
  344  ls
  345  pushd /nanopore/cgl/glenn-scratch/split
  346  ls
  347  pwd
  348  rsynnc *.maf.gz hgwdev:/hive/users/markd/compartiveGenomics/projs/alignments/447-mammalian-2022v1/
  349  rsync *.maf.gz hgwdev:/hive/users/markd/compartiveGenomics/projs/alignments/447-mammalian-2022v1/
  350  rsync 447-mammalian-2022v1.chr22.maf.gz hgwdev:/hive/users/markd/compartiveGenomics/projs/alignments/447-mammalian-2022v1/
  351  id
  352  group
  353  groups
  354  lid 
  355  members
  356  lid -g wet
  357  pwd
  358  popd
  359  pwd
  360  ls
  361  cd 241-mammalian-2020v2-hub/
  362  ls
  363  pwd
  364  ls -1  */corces2020_caudate.*.bb
  365  pwd
  366  git pull
  367  mmake
  368  pwd
  369  cd ../..
  370  pwd
  371  ls
  372  ./makeBackup 
  373  pwd
  374  ls
  375  d
  376  pwd
  377  ls
  378  pip install --upgrade pipettor
  379  pwd
  380  ls
  381  pwd
  382  gps apache
  383  ls
  384  ps -i
  385  ls
  386  file *
  387  file NLA_chm13_up_20+80k_hg38_chr1_bigPsl.bb 
  388  pwd
  389  popd
  390  pwd
  391  ls
  392  pushd
  393  pwd
  394  pushd ~
  395  pwd
  396  cd compbio/kznf/
  397  ls
  398  cd projs/
  399  ls
  400  l
  401  pip install --upgrade flake8
  402  pwd
  403  pushd
  404  pwd
  405  popd
  406  cd primate-hub/
  407  ls
  408  git pull
  409  cd hubs/2020-10/
  410  ls
  411  cd asm-hub/
  412  make -n
  413  mmake 
  414  pwd
  415  cd ../track-hub/
  416  ls
  417  mmake
  418  pwd
  419  ls
  420  ls trackDb/
  421  git pull
  422  mmake
  423  pwd
  424  emacs -nw
  425  top
  426  fg
  427  top
  428  fg
  429  cd ~/compbio/code/pycbio/
  430  git pull
  431  pwd
  432  ppwd
  433  pip --version
  434  ls
  435  pio install -r requirements.txt 
  436  pip install -r requirements.txt 
  437  pwd
  438  ln -s /public/home/markd/compbio/code/pycbio/lib/pycbio ~/opt/current/x86_64/lib/python3.11/site-packages/
  439  pip install --upgrade pipettor
  440  id
  441  pwd
  442  git pull
  443  git pull --tags
  444  git pull -f --tags
  445  pwd
  446  signver 
  447  pwd
  448  ls
  449  which docker
  450  ls /usr/bin/git
  451  uname -a
  452  ls /data/
  453  ls /public/groups/
  454  ls /public/groups/cgl/
  455  ls /public/groups/cgl/local/
  456  ls /public/groups/cgl/local/bin/
  457   /public/groups/cgl/local/bin/perl --version
  458  which python
  459  psi -u
  460  ls
  461  pwd
  462  who
  463  uptime
  464  cd /public/home/markd/kent/src
  465  nice jkmmake clean &>log &
  466  ]
  467  nice jkmmake  &>log &
  468  cd ~/public_html/
  469  ls
  470  cd primates-hubs/
  471  ls
  472  l
  473  ls /public/groups/hausslerlab/
  474  [wd
  475  pwd
  476  ls
  477  cd 2020-10/
  478  pwd
  479  ls
  480  cd track-hub/
  481  ls
  482  pwd
  483  emacs -nw
  484  ssh-sh
  485  emacs -nw
  486  ls
  487  which emacs
  488  screen
  489  which anaconda
  490  python3 --version
  491  pip
  492  which pip
  493  w
  494  w
  495  w
  496  w
  497  ls
  498  ls
  499  which condaenv 
  500   condaenv 
  501  exit
  502  exec env TERM='dumb' INSIDE_EMACS='29.0.60,tramp:2.6.0.29.1' ENV='' HISTFILE=~/.tramp_history PROMPT_COMMAND='' PS1=///a10ddbe6879e467e12c7ccb2a5cb04bf\#\$ PS2='' PS3='' /bin/sh  -i
  503  command dirs
  504  taffy veiw -h
  505  taffy view -h
  506  tabix -h
  507  taffy normalize
  508  taffy norm -h
  509  df -h /dev/shm/
  510  df -hl
  511  (zcat  ../Gallus_gallus/Gallus_gallus.maf.gz| taffy view  | taffy norm --maf >/dev/shm/Gallus_gallus.norm.maf)>&log&
  512  l
  513  psi
  514  taffy --version
  515  taffy -h
  516  pushd ~/tmp/taffy/
  517  git status
  518  git info  .
  519  git log -h
  520  git log |head
  521  psi
  522  df -h
  523  df /dev/shm/
  524  df -l /dev/shm/
  525  fg
  526  rm /dev/shm/Gallus_gallus.norm.maf 
  527  (zcat  ../Gallus_gallus/Gallus_gallus.maf.gz| taffy view  | taffy norm --maf | pigz -c >Gallus_gallus.norm.maf.gz)>&log&
  528  cat log
  529  pwd
  530  pushd
  531  (zcat  ../Gallus_gallus/Gallus_gallus.maf.gz| taffy view  | taffy norm --maf | pigz -c >Gallus_gallus.norm.maf.gz)>&log&
  532  wait
  533  h >h