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PacificBiosciences / FALCON-integrate

Mostly deprecated. See https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
https://github.com/PacificBiosciences/FALCON/wiki/Manual
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Install problem : nim: Command not found #157

Closed Fyphia closed 6 years ago

Fyphia commented 7 years ago

Hi, I'm trying to install the latest Falcon according to
https://github.com/PacificBiosciences/FALCON-integrate/wiki/Installation as follow:

export GIT_SYM_CACHE_DIR=~/.git-sym-cache # to speed things up
git clone git://github.com/PacificBiosciences/FALCON-integrate.git
cd FALCON-integrate
git checkout develop  # or whatever version you want
git submodule update --init --recursive # Note: You must do this yourself! No longer via `make init`.
make init
source env.sh
make config-edit-user
make -j all
make test  # to run a simple one

My python version is 2.7.12.

When I run make -j all, the output is as follows:

make -C ./FALCON-make/ all
make[1]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/FALCON-make'
make show
make[2]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/FALCON-make'
mkdir -p /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/bin
which python
/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/bin/python
echo "PYTHONUSERBASE=/rhome/fxie/bigdata/new2/FALCON-integrate/fc_env"
PYTHONUSERBASE=/rhome/fxie/bigdata/new2/FALCON-integrate/fc_env
python -c 'import site; print site.USER_BASE'
/rhome/fxie/bigdata/new2/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 `/bigdata/baolab/fxie/new2/FALCON-integrate/FALCON-make'
make install-pip
make[2]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/FALCON-make'
python -c 'import pip; print pip' || python get-pip.py --user
<module 'pip' from '/opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/lib/python2.7/site-packages/pip-8.1.2-py2.7.egg/pip/__init__.pyc'>
pip install --user --upgrade pip
Collecting pip
  Using cached pip-9.0.1-py2.py3-none-any.whl
Installing collected packages: pip
Successfully installed pip-8.1.2
You are using pip version 8.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
pip install --user --upgrade setuptools # needed when --edit is used
Requirement already up-to-date: setuptools in /bigdata/baolab/fxie/new2/FALCON-integrate/fc_env/lib/python2.7/site-packages
You are using pip version 8.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
pip install --user nose pytest # for running tests while building
Requirement already satisfied (use --upgrade to upgrade): nose in /bigdata/baolab/fxie/new2/FALCON-integrate/fc_env/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): pytest in /bigdata/baolab/fxie/new2/FALCON-integrate/fc_env/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): setuptools in /bigdata/baolab/fxie/new2/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest)
Requirement already satisfied (use --upgrade to upgrade): py>=1.4.33 in /bigdata/baolab/fxie/new2/FALCON-integrate/fc_env/lib/python2.7/site-packages (from pytest)
You are using pip version 8.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
make[2]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/FALCON-make'
make install # This will double -D_GNU_SOURCE, but that is ok for now.
make[2]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/FALCON-make'
make -C /rhome/fxie/bigdata/new2/FALCON-integrate/DAZZ_DB all
make -C /rhome/fxie/bigdata/new2/FALCON-integrate/DAMASKER all
make -C /rhome/fxie/bigdata/new2/FALCON-integrate/DEXTRACTOR all
cd /rhome/fxie/bigdata/new2/FALCON-integrate/pypeFLOW; pip uninstall -v .; pip install -v --user --edit .
# TODO: copy vs. symlink?
make -C /rhome/fxie/bigdata/new2/FALCON-integrate/nim-falcon/src -j1 all
ln -sf /rhome/fxie/bigdata/new2/FALCON-integrate/git-sym/git-sym /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/bin/git-sym
make[3]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DAMASKER'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DAMASKER'
make[3]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DEXTRACTOR'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DEXTRACTOR'
PREFIX=/rhome/fxie/bigdata/new2/FALCON-integrate/fc_env make -C /rhome/fxie/bigdata/new2/FALCON-integrate/DAMASKER symlink
PREFIX=/rhome/fxie/bigdata/new2/FALCON-integrate/fc_env make -C /rhome/fxie/bigdata/new2/FALCON-integrate/DEXTRACTOR symlink
make[3]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB'
PREFIX=/rhome/fxie/bigdata/new2/FALCON-integrate/fc_env make -C /rhome/fxie/bigdata/new2/FALCON-integrate/DAZZ_DB symlink
make[3]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/nim-falcon/src'
nim --threads:on --threadAnalysis:off --verbosity:2 -d:release  --tlsemulation:on --out:fc_rr_hctg_track2.exe c fc_rr_hctg_track2.nim
make[3]: nim: Command not found
make[3]: *** [fc_rr_hctg_track2.exe] Error 127
make[3]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/nim-falcon/src'
make[2]: *** [install-nim-falcon] Error 2
make[2]: *** Waiting for unfinished jobs....
make[3]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DAMASKER'
ln -sf /bigdata/baolab/fxie/new2/FALCON-integrate/DAMASKER/datander /bigdata/baolab/fxie/new2/FALCON-integrate/DAMASKER/TANmask /bigdata/baolab/fxie/new2/FALCON-integrate/DAMASKER/REPmask /bigdata/baolab/fxie/new2/FALCON-integrate/DAMASKER/HPC.TANmask /bigdata/baolab/fxie/new2/FALCON-integrate/DAMASKER/HPC.REPmask /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/bin
make[3]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB'
ln -sf /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/fasta2DB /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/DB2fasta /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/DBsplit /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/DBdust /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/Catrack /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/DBshow /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/DBstats /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/DBrm /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/simulator /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/fasta2DAM /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/DAM2fasta /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/DBdump /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/rangen /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/bin
make[3]: Entering directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DEXTRACTOR'
ln -sf /bigdata/baolab/fxie/new2/FALCON-integrate/DEXTRACTOR/dexta /bigdata/baolab/fxie/new2/FALCON-integrate/DEXTRACTOR/undexta /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/bin
make[3]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DEXTRACTOR'
make[3]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DAMASKER'
ln -sf /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/libdazzdb.a /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/lib
ln -sf /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/DB.h /bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB/QV.h /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/include
make[3]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/DAZZ_DB'
You are using pip version 8.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Obtaining file:///bigdata/baolab/fxie/new2/FALCON-integrate/pypeFLOW
  Running setup.py (path:/bigdata/baolab/fxie/new2/FALCON-integrate/pypeFLOW/setup.py) egg_info for package from file:///bigdata/baolab/fxie/new2/FALCON-integrate/pypeFLOW
    Running command python setup.py egg_info
    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 /bigdata/baolab/fxie/new2/FALCON-integrate/pypeFLOW has version 1.0.0, which satisfies requirement pypeflow==1.0.0 from file:///bigdata/baolab/fxie/new2/FALCON-integrate/pypeFLOW
Requirement already satisfied (use --upgrade to upgrade): networkx<=1.11,>=1.7 in /opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/lib/python2.7/site-packages (from pypeflow==1.0.0)
Requirement already satisfied (use --upgrade to upgrade): decorator>=3.4.0 in /opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/lib/python2.7/site-packages (from networkx<=1.11,>=1.7->pypeflow==1.0.0)
Installing collected packages: pypeflow
  Running setup.py develop for pypeflow
    Running command /opt/linux/centos/7.x/x86_64/pkgs/python/2.7.12/bin/python -c "import setuptools, tokenize;__file__='/bigdata/baolab/fxie/new2/FALCON-integrate/pypeFLOW/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" develop --no-deps --user --prefix=
    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 /bigdata/baolab/fxie/new2/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow.egg-link (link to .)
    pypeflow 1.0.0 is already the active version in easy-install.pth
    Installing pwatcher-pypeflow-example script to /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/bin
    Installing heartbeat-wrapper script to /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/bin
    Installing pwatcher-main script to /rhome/fxie/bigdata/new2/FALCON-integrate/fc_env/bin

    Installed /bigdata/baolab/fxie/new2/FALCON-integrate/pypeFLOW
Successfully installed pypeflow-1.0.0
Cleaning up...
You are using pip version 8.1.2, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
make[2]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/FALCON-make'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/FALCON-make'
make: *** [all] Error 2

It seems something wrong in make[3]: nim: Command not found make[3]: ** [fc_rr_hctg_track2.exe] Error 127 make[3]: Leaving directory `/bigdata/baolab/fxie/new2/FALCON-integrate/nim-falcon/src' make[2]: [install-nim-falcon] Error 2**

Can anybody help me with this issue ? Thanks a lot !

iggyB commented 7 years ago

Hi,

You will need to install nim compiler: https://nim-lang.org/

Cheers, Iggy

rick-heig commented 6 years ago

Hello. I was running in the same issue, however once nim was installed I stumbled on the following error : 

/FALCON/FALCON-integrate/nim-falcon/repos/msgpack4nim/msgpack4nim.nim(27, 32) Error: cannot open 'deques'
  import tables, intsets, lists, deques, sets, strtabs, critbits, macros
                                 ^
makefile:41: recipe for target 'fc_rr_hctg_track2.exe' failed
make[3]: *** [fc_rr_hctg_track2.exe] Error 1

I am also running Python 2.7.12 and nim version 0.12.0 on a Linux 4.4.0 Kernel (64bit)

Can anybody help me finish the installation process ? Thanks.

Fyphia commented 6 years ago

hello,

You can try to install nim in your system in another folder instead of /nim-falcon/, and add its path to system. Find nim in its github address.

Fyphia

------------------ 原始邮件 ------------------ 发件人: "rick-heig"notifications@github.com; 发送时间: 2018年4月23日(星期一) 下午3:36 收件人: "PacificBiosciences/FALCON-integrate"FALCON-integrate@noreply.github.com; 抄送: "解菲"270488878@qq.com; "Author"author@noreply.github.com; 主题: Re: [PacificBiosciences/FALCON-integrate] Install problem : nim:Command not found (#157)

Hello. I was running in the same issue, however once nim was installed I stumbled on the following error : /FALCON/FALCON-integrate/nim-falcon/repos/msgpack4nim/msgpack4nim.nim(27, 32) Error: cannot open 'deques' import tables, intsets, lists, deques, sets, strtabs, critbits, macros ^ makefile:41: recipe for target 'fc_rr_hctg_track2.exe' failed make[3]: *** [fc_rr_hctg_track2.exe] Error 1
I am also running Python 2.7.12 and nim version 0.12.0 on a Linux 4.4.0 Kernel (64bit)

Can anybody help me finish the installation process ? Thanks.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

OPSmolander commented 6 years ago

I have the same problem and I've tried installing nim from github and from apt and neither works. I am running Ubuntu 16.04. I have been previously able to install Falcon without any major problems. I have also Anaconda 2.7 installed.

pb-cdunn commented 6 years ago

@OPSmolander, which problem precisely? Missing nim? Or the problem with deque?

I had to lock to an older version of msgpack4nim, so you might try a fresh install of nim-falcon (dev branch).

OPSmolander commented 6 years ago

@pb-cdunn The problem with the deque. If I remove the system nim then I get the error with missing nim. If I install nim then I will get the problem with deque.. What do you mean with fresh install of nim-falcon and dev branch? I seem to find only master-branch for nim-falcon.

pb-cdunn commented 6 years ago

Where do you get nim-falcon? dev branch is here: https://github.com/bio-nim/nim-falcon/tree/dev

OPSmolander commented 6 years ago

I have been trying to get this work now using that dev branch of nim-falcon but ended up with this:

/home/opsmolan/FALCON-integrate/nim-falcon/repos/msgpack4nim/msgpack4nim.nim(623, 40) Error: undeclared identifier: 'SomeFloat' proc pack_type*(s: var MsgStream, val: SomeFloat) = ^ makefile:41: recipe for target 'fc_rr_hctg_track2.exe' failed make[3]: [fc_rr_hctg_track2.exe] Error 1 make[3]: Leaving directory '/home/opsmolan/FALCON-integrate/nim-falcon/src' makefile:44: recipe for target 'install-nim-falcon' failed make[2]: [install-nim-falcon] Error 2 make[2]: *** Waiting for unfinished jobs....

If there was any suggestion how to get the fresh install of nim-falcon working properly, I would really appreciate.

ghannum commented 6 years ago

I am having the same problems as @OPSmolander. Is there an updated Dockerfile I can reference? The one in the official wiki seems out-of-date.

pb-cdunn commented 6 years ago

Which wiki? Which Dockerfile?

If you have a problem with nim, you need to tell us your version of nim.

$ nim --version
Nim Compiler Version 0.18.1 [Linux: amd64]
Compiled at 2018-05-15
Copyright (c) 2006-2018 by Andreas Rumpf

git hash: 02f01470ab46067c18535605179b95b143b1e25f
pb-cdunn commented 6 years ago

Also, which git SHA1 for FALCON-integrate and nim-falcon?

ghannum commented 6 years ago

@pb-cdunn Here is the wiki with an old Falcon Dockerfile: https://github.com/PacificBiosciences/FALCON/wiki/Falcon-as-a-Docker-container

Nim Compiler Version 0.12.0 (2015-11-02) [Linux: amd64] Copyright (c) 2006-2015 by Andreas Rumpf active boot switches: -d:release

FALCON-integrate hash: ad6479b nim-falcon hash: 821a311

pb-cdunn commented 6 years ago

You need a more recent nim installation. Version 0.18.1 works for me.

I guess that Docker container needs to be updated.

EbubeUd commented 3 years ago

Hello, I had the same problem. If you are on windows, you can install nim Using chocolate.

Open Powershell as an administrator and run "choco install nim"

This should have it set up properly for you. Including the environment variables.