There us no "activate" file. Installation error?

[Jung19911124]

Hi, I am trying to use Falcon_unzip on HGAP4 output for comparison.

Following the instruction here https://github.com/PacificBiosciences/FALCON-integrate/wiki/Installation, I tried to install Falcon_unzip. Then, I got message below.

I thought this was successful and proceeded to run hgap4_adapt followong the instruction here http://pb-falcon.readthedocs.io/en/latest/hgap4_adapt.html#running-falcon-unzip.

However, I happened to find there is no "activate" file in fc_env/bin directory.

What I have to do ? Any comments would be appreciated.

Best, Jung

installation process

make -C ./FALCON-make/ all make[1]: Entering directory /home/jung/Tools/FALCON-integrate/FALCON-make' make show make[2]: Entering directory/home/jung/Tools/FALCON-integrate/FALCON-make' mkdir -p /home/jung/Tools/FALCON-integrate/fc_env/bin which python /home/jung/.pyenv/shims/python echo "PYTHONUSERBASE=/home/jung/Tools/FALCON-integrate/fc_env" PYTHONUSERBASE=/home/jung/Tools/FALCON-integrate/fc_env python -c 'import site; print site.USER_BASE' /home/jung/Tools/FALCON-integrate/fc_env echo "FALCON_PIP_EDIT=--edit" FALCON_PIP_EDIT=--edit echo "FALCON_PIP_USER=--user" FALCON_PIP_USER=--user make[2]: Leaving directory /home/jung/Tools/FALCON-integrate/FALCON-make' make install-pip make[2]: Entering directory/home/jung/Tools/FALCON-integrate/FALCON-make' python -c 'import pip; print pip' || python get-pip.py --user <module 'pip' from '/home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages/pip/init.pyc'> pip install --user --upgrade pip Requirement already up-to-date: pip in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages pip install --user --upgrade setuptools # needed when --edit is used Requirement already up-to-date: setuptools in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages pip install --user nose pytest # for running tests while building Requirement already satisfied: nose in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages Requirement already satisfied: pytest in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages Requirement already satisfied: six>=1.10.0 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from pytest) Requirement already satisfied: attrs>=17.4.0 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from pytest) Requirement already satisfied: setuptools in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from pytest) Requirement already satisfied: funcsigs; python_version < "3.0" in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from pytest) Requirement already satisfied: py>=1.5.0 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from pytest) Requirement already satisfied: more-itertools>=4.0.0 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from pytest) Requirement already satisfied: pluggy<0.7,>=0.5 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from pytest) make[2]: Leaving directory /home/jung/Tools/FALCON-integrate/FALCON-make' make install # This will double -D_GNU_SOURCE, but that is ok for now. make[2]: Entering directory/home/jung/Tools/FALCON-integrate/FALCON-make' make -C /home/jung/Tools/FALCON-integrate/DAZZ_DB all make -C /home/jung/Tools/FALCON-integrate/DAMASKER all make -C /home/jung/Tools/FALCON-integrate/DEXTRACTOR all cd /home/jung/Tools/FALCON-integrate/pypeFLOW; pip uninstall -v .; pip install -v --user --edit .

TODO: copy vs. symlink?

make -C /home/jung/Tools/FALCON-integrate/nim-falcon/src -j1 all ln -sf /home/jung/Tools/FALCON-integrate/git-sym/git-sym /home/jung/Tools/FALCON-integrate/fc_env/bin/git-sym make[3]: Entering directory /home/jung/Tools/FALCON-integrate/DEXTRACTOR' make[3]: Nothing to be done forall'. make[3]: Leaving directory /home/jung/Tools/FALCON-integrate/DEXTRACTOR' PREFIX=/home/jung/Tools/FALCON-integrate/fc_env make -C /home/jung/Tools/FALCON-integrate/DEXTRACTOR symlink make[3]: Entering directory/home/jung/Tools/FALCON-integrate/DEXTRACTOR' ln -sf /home/jung/Tools/FALCON-integrate/DEXTRACTOR/dexta /home/jung/Tools/FALCON-integrate/DEXTRACTOR/undexta /home/jung/Tools/FALCON-integrate/fc_env/bin make[3]: Entering directory /home/jung/Tools/FALCON-integrate/DAMASKER' make[3]: Nothing to be done forall'. make[3]: Leaving directory /home/jung/Tools/FALCON-integrate/DAMASKER' PREFIX=/home/jung/Tools/FALCON-integrate/fc_env make -C /home/jung/Tools/FALCON-integrate/DAMASKER symlink make[3]: Entering directory/home/jung/Tools/FALCON-integrate/DAMASKER' ln -sf /home/jung/Tools/FALCON-integrate/DAMASKER/datander /home/jung/Tools/FALCON-integrate/DAMASKER/TANmask /home/jung/Tools/FALCON-integrate/DAMASKER/REPmask /home/jung/Tools/FALCON-integrate/DAMASKER/HPC.TANmask /home/jung/Tools/FALCON-integrate/DAMASKER/HPC.REPmask /home/jung/Tools/FALCON-integrate/fc_env/bin make[3]: Leaving directory /home/jung/Tools/FALCON-integrate/DAMASKER' make[3]: Leaving directory/home/jung/Tools/FALCON-integrate/DEXTRACTOR' make[3]: Entering directory /home/jung/Tools/FALCON-integrate/DAZZ_DB' make[3]: Nothing to be done forall'. make[3]: Leaving directory /home/jung/Tools/FALCON-integrate/DAZZ_DB' PREFIX=/home/jung/Tools/FALCON-integrate/fc_env make -C /home/jung/Tools/FALCON-integrate/DAZZ_DB symlink make[3]: Entering directory/home/jung/Tools/FALCON-integrate/DAZZ_DB' ln -sf /home/jung/Tools/FALCON-integrate/DAZZ_DB/fasta2DB /home/jung/Tools/FALCON-integrate/DAZZ_DB/DB2fasta /home/jung/Tools/FALCON-integrate/DAZZ_DB/DBsplit /home/jung/Tools/FALCON-integrate/DAZZ_DB/DBdust /home/jung/Tools/FALCON-integrate/DAZZ_DB/Catrack /home/jung/Tools/FALCON-integrate/DAZZ_DB/DBshow /home/jung/Tools/FALCON-integrate/DAZZ_DB/DBstats /home/jung/Tools/FALCON-integrate/DAZZ_DB/DBrm /home/jung/Tools/FALCON-integrate/DAZZ_DB/simulator /home/jung/Tools/FALCON-integrate/DAZZ_DB/fasta2DAM /home/jung/Tools/FALCON-integrate/DAZZ_DB/DAM2fasta /home/jung/Tools/FALCON-integrate/DAZZ_DB/DBdump /home/jung/Tools/FALCON-integrate/DAZZ_DB/rangen /home/jung/Tools/FALCON-integrate/fc_env/bin ln -sf /home/jung/Tools/FALCON-integrate/DAZZ_DB/libdazzdb.a /home/jung/Tools/FALCON-integrate/fc_env/lib ln -sf /home/jung/Tools/FALCON-integrate/DAZZ_DB/DB.h /home/jung/Tools/FALCON-integrate/DAZZ_DB/QV.h /home/jung/Tools/FALCON-integrate/fc_env/include make[3]: Leaving directory /home/jung/Tools/FALCON-integrate/DAZZ_DB' make -C /home/jung/Tools/FALCON-integrate/DALIGNER all make[3]: Entering directory/home/jung/Tools/FALCON-integrate/nim-falcon/src' make[3]: Nothing to be done for all'. make[3]: Leaving directory/home/jung/Tools/FALCON-integrate/nim-falcon/src' rsync /home/jung/Tools/FALCON-integrate/nim-falcon/src/*.exe /home/jung/Tools/FALCON-integrate/fc_env/bin/ make[3]: Entering directory /home/jung/Tools/FALCON-integrate/DALIGNER' make[3]: Nothing to be done forall'. make[3]: Leaving directory /home/jung/Tools/FALCON-integrate/DALIGNER' PREFIX=/home/jung/Tools/FALCON-integrate/fc_env make -C /home/jung/Tools/FALCON-integrate/DALIGNER symlink make[3]: Entering directory/home/jung/Tools/FALCON-integrate/DALIGNER' ln -sf /home/jung/Tools/FALCON-integrate/DALIGNER/daligner /home/jung/Tools/FALCON-integrate/DALIGNER/HPC.daligner /home/jung/Tools/FALCON-integrate/DALIGNER/LAsort /home/jung/Tools/FALCON-integrate/DALIGNER/LAmerge /home/jung/Tools/FALCON-integrate/DALIGNER/LAsplit /home/jung/Tools/FALCON-integrate/DALIGNER/LAcat /home/jung/Tools/FALCON-integrate/DALIGNER/LAshow /home/jung/Tools/FALCON-integrate/DALIGNER/LAdump /home/jung/Tools/FALCON-integrate/DALIGNER/LAcheck /home/jung/Tools/FALCON-integrate/DALIGNER/LAindex /home/jung/Tools/FALCON-integrate/DALIGNER/daligner_p /home/jung/Tools/FALCON-integrate/DALIGNER/LA4Falcon /home/jung/Tools/FALCON-integrate/DALIGNER/LA4Ice /home/jung/Tools/FALCON-integrate/DALIGNER/DB2Falcon /home/jung/Tools/FALCON-integrate/fc_env/bin make[3]: Leaving directory `/home/jung/Tools/FALCON-integrate/DALIGNER' Obtaining file:///home/jung/Tools/FALCON-integrate/pypeFLOW Running setup.py (path:/home/jung/Tools/FALCON-integrate/pypeFLOW/setup.py) egg_info for package from file:///home/jung/Tools/FALCON-integrate/pypeFLOW Running command python setup.py egg_info /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages/setuptools/dist.py:397: UserWarning: Normalizing '2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef ' to '2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef' normalized_version, running egg_info writing requirements to pypeflow.egg-info/requires.txt writing pypeflow.egg-info/PKG-INFO writing top-level names to pypeflow.egg-info/top_level.txt writing dependency_links to pypeflow.egg-info/dependency_links.txt writing entry points to pypeflow.egg-info/entry_points.txt reading manifest file 'pypeflow.egg-info/SOURCES.txt' writing manifest file 'pypeflow.egg-info/SOURCES.txt' Source in /home/jung/Tools/FALCON-integrate/pypeFLOW has version 2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef, which satisfies requirement pypeflow==2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef from file:///home/jung/Tools/FALCON-integrate/pypeFLOW Requirement already satisfied: networkx<=1.11,>=1.7 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from pypeflow==2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef) Requirement already satisfied: future>=0.16.0 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from pypeflow==2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef) Requirement already satisfied: decorator>=3.4.0 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from networkx<=1.11,>=1.7->pypeflow==2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef) Installing collected packages: pypeflow Found existing installation: pypeflow 2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef Uninstalling pypeflow-2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef: Removing file or directory /home/jung/Tools/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow.egg-link Removing pth entries from /home/jung/Tools/FALCON-integrate/fc_env/lib/python2.7/site-packages/easy-install.pth: Removing entry: /home/jung/Tools/FALCON-integrate/pypeFLOW Successfully uninstalled pypeflow-2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef Running setup.py develop for pypeflow Running command /home/jung/.pyenv/versions/2.7.9/bin/python2.7 -c "import setuptools, tokenize;file='/home/jung/Tools/FALCON-integrate/pypeFLOW/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" develop --no-deps --user --prefix= /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages/setuptools/dist.py:397: UserWarning: Normalizing '2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef ' to '2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef' normalized_version, running develop running egg_info writing requirements to pypeflow.egg-info/requires.txt writing pypeflow.egg-info/PKG-INFO writing top-level names to pypeflow.egg-info/top_level.txt writing dependency_links to pypeflow.egg-info/dependency_links.txt writing entry points to pypeflow.egg-info/entry_points.txt reading manifest file 'pypeflow.egg-info/SOURCES.txt' writing manifest file 'pypeflow.egg-info/SOURCES.txt' running build_ext Creating /home/jung/Tools/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow.egg-link (link to .) Adding pypeflow 2.0.1+git.cfb4aceb07ef56f9e1250d6abe123ef9a31762ef to easy-install.pth file Installing pwatcher-pypeflow-example script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing heartbeat-wrapper script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing pwatcher-main script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installed /home/jung/Tools/FALCON-integrate/pypeFLOW Successfully installed pypeflow Cleaning up... cd /home/jung/Tools/FALCON-integrate/FALCON; pip uninstall -v .; pip install -v --user --edit . Obtaining file:///home/jung/Tools/FALCON-integrate/FALCON Running setup.py (path:/home/jung/Tools/FALCON-integrate/FALCON/setup.py) egg_info for package from file:///home/jung/Tools/FALCON-integrate/FALCON Running command python setup.py egg_info /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages/setuptools/dist.py:397: UserWarning: Normalizing '1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382 ' to '1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382' normalized_version, running egg_info writing requirements to falcon_kit.egg-info/requires.txt writing falcon_kit.egg-info/PKG-INFO writing top-level names to falcon_kit.egg-info/top_level.txt writing dependency_links to falcon_kit.egg-info/dependency_links.txt writing entry points to falcon_kit.egg-info/entry_points.txt reading manifest file 'falcon_kit.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'falcon_kit.egg-info/SOURCES.txt' Source in /home/jung/Tools/FALCON-integrate/FALCON has version 1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382, which satisfies requirement falcon-kit==1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382 from file:///home/jung/Tools/FALCON-integrate/FALCON Requirement already satisfied: networkx<=1.11,>=1.7 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from falcon-kit==1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382) Requirement already satisfied: msgpack in /home/jung/Tools/FALCON-integrate/fc_env/lib/python2.7/site-packages (from falcon-kit==1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382) Requirement already satisfied: future>=0.16.0 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from falcon-kit==1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382) Requirement already satisfied: pypeFLOW>=2.0.0 in /home/jung/Tools/FALCON-integrate/pypeFLOW (from falcon-kit==1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382) Requirement already satisfied: decorator>=3.4.0 in /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages (from networkx<=1.11,>=1.7->falcon-kit==1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382) Installing collected packages: falcon-kit Found existing installation: falcon-kit 1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382 Uninstalling falcon-kit-1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382: Removing file or directory /home/jung/Tools/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon-kit.egg-link Removing pth entries from /home/jung/Tools/FALCON-integrate/fc_env/lib/python2.7/site-packages/easy-install.pth: Removing entry: /home/jung/Tools/FALCON-integrate/FALCON Successfully uninstalled falcon-kit-1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382 Running setup.py develop for falcon-kit Running command /home/jung/.pyenv/versions/2.7.9/bin/python2.7 -c "import setuptools, tokenize;file='/home/jung/Tools/FALCON-integrate/FALCON/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" develop --no-deps --user --prefix= /home/jung/.pyenv/versions/2.7.9/lib/python2.7/site-packages/setuptools/dist.py:397: UserWarning: Normalizing '1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382 ' to '1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382' normalized_version, running develop running egg_info writing requirements to falcon_kit.egg-info/requires.txt writing falcon_kit.egg-info/PKG-INFO writing top-level names to falcon_kit.egg-info/top_level.txt writing dependency_links to falcon_kit.egg-info/dependency_links.txt writing entry points to falcon_kit.egg-info/entry_points.txt reading manifest file 'falcon_kit.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'falcon_kit.egg-info/SOURCES.txt' running build_ext copying build/lib.linux-x86_64-2.7/ext_falcon.so -> Creating /home/jung/Tools/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon-kit.egg-link (link to .) Adding falcon-kit 1.0+git.c1e0d45f1b847f572cd9834576154ae44bbd7382 to easy-install.pth file Installing fc_fetch_reads script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_pr_ctg_track script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_actg_coordinate script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_fasta2fasta script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_run.py script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_ctg_link_analysis script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_ovlp_to_graph script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_gen_gfa_v1 script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_ovlp_filter script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_get_read_ctg_map script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_run script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_contig_annotate script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_graph_to_utgs script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_run1 script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_ovlp_stats script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_consensus script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_rr_ctg_track script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_calc_cutoff script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing falcon-task script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_graph_to_contig script to /home/jung/Tools/FALCON-integrate/fc_env/bin Installing fc_dedup_a_tigs script to /home/jung/Tools/FALCON-integrate/fc_env/bin

Installed /home/jung/Tools/FALCON-integrate/FALCON Successfully installed falcon-kit Cleaning up... make[2]: Leaving directory /home/jung/Tools/FALCON-integrate/FALCON-make' make check make[2]: Entering directory/home/jung/Tools/FALCON-integrate/FALCON-make' python -c 'import pypeflow.simple_pwatcher_bridge; print pypeflow.simple_pwatcher_bridge' <module 'pypeflow.simple_pwatcher_bridge' from '/home/jung/Tools/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.pyc'> python -c 'import falcon_kit; print falcon_kit.falcon' <CDLL '/home/jung/Tools/FALCON-integrate/FALCON/ext_falcon.so', handle 18fd1d0 at 2ac6464b18d0> make[2]: Leaving directory /home/jung/Tools/FALCON-integrate/FALCON-make' make[1]: Leaving directory/home/jung/Tools/FALCON-integrate/FALCON-make'

[pb-cdunn]

The activate file will exist only if you set up your own virtualenv. You'll have to google that. PYTHONUSERBASE is another option.